% ACM Transactions on Mathematical Software.
@STRING{acmtms      = "ACM Trans. Maths. Softw."}

% Analytical Chemistry.
@STRING{ac          = "Anal. Chem."}

% Annalen der Physik.
@STRING{ap          = "Ann. Physik"}

% Annals of Mathematical Statistics.
@STRING{ams         = "Ann. Math. Stat."}

% Annals of Statistics.
@STRING{anstat      = "Ann. Stat."}

% Applied Magnetic Resonance.
@STRING{amr         = "Appl. Magn. Reson."}

% Biochemistry.
@STRING{biochem     = "Biochemistry"}

% Bioinformatics.
@STRING{bioinformatics = "Bioinformatics"}

% Biometrika.
@STRING{biometrika  = "Biometrika"}

% Biophysical journal.
@STRING{bj          = "Biophys. J."}

% Chemistry - A European Journal.
@STRING{cej         = "Chem. Eur. J."}

% The Computer Journal.
@STRING{cj          = "Comp. J."}

% Chemistry Review.
@STRING{cr          = "Chem. Rev."}

% European Journal of Biochemistry.
@STRING{ejb         = "Eur. J. Biochem."}

% Journal of the American Chemical Society.
@STRING{jacs        = "J. Am. Chem. Soc."}

% Journal of Biomolecular NMR.
@STRING{jbnmr       = "J. Biomol. NMR"}

% Journal of Biomolecular Structural Dynamics?
@STRING{jbsd        = "J. Biomol. Struct. Dyn."}

% Journal of Chemical Physics.
@STRING{jcp         = "J. Chem. Phys."}

% Journal of the Institue of Mathematics and its Applications.
@STRING{jima        = "J. Inst. Maths. Applics."}

% Journal of Molecular Biology.
@STRING{jmb         = "J. Mol. Biol."}

% Journal of Mathematical Psychology?
@STRING{jmp         = "J. Math. Psychol."}

% Journal of Magnetic Resonance?
@STRING{jmr         = "J. Magn. Reson."}

% Journal of Magnetic Resonance B?
@STRING{jmrb        = "J. Magn. Reson. B"}

% Journal de Physique et le Radium.
@STRING{jpr         = "J. Phys. Radium"}

% Journal of Research of the National Bureau of Standards.
@STRING{jrnbs       = "J. Res. Natn. Bur. Stand."}

% Molecular BioSystems.
@STRING{mb          = "Mol. BioSyst."}

% Mathematics of Computation.
@STRING{mc          = "Math. Comp."}

% Molecular Physics.
@STRING{mp          = "Mol. Phys."}

% Physical Review.
@STRING{physrev     = "Phys. Rev."}

% Progress in Nuclear Magnetic Resonance Spectroscopy.
@STRING{pnmrs       = "Prog. NMR Spectrosc."}

% Quarterly of Applied Mathematics.
@STRING{qam         = "Quarterly of Applied Mathematics"}

% Science.
@STRING{sci         = "Science"}

% SIAM Journal.
@STRING{siamj       = "SIAM J."}

% SIAM Journal on Numerical Analysis.
@STRING{siamjna     = "SIAM J. Numer. Anal."}



@Book{Abragam61,
  Author         = {Abragam, Anatole},
  Title          = {The Principles of Nuclear Magnetism},
  Publisher      = {Clarendon Press},
  Address        = {Oxford},
  year           = 1961
}

@InProceedings{Akaike73,
  Author         = {Akaike, H.},
  Title          = {Information theory and an extension of the maximum
                   likelihood principle},
  BookTitle      = {Proceedings of the {S}econd {I}nternational
                   {S}ymposium on {I}nformation {T}heory},
  Editor         = {Petrov, B. N. and Csaki, F.},
  Pages          = {267-281},
  Address        = {Budapest},
  Publisher      = {Akademia Kiado},
  abstract       = {In this paper it is shown that the classical maximum
                   likelihood principle can be considered to be a method
                   of asymptotic realization of an optimum estimate with
                   respect to a very general information theoretic
                   criterion. This observation allows an extension of the
                   principle to provide answers to many practical problems
                   of statistical model fitting.},
  keywords       = {asymptotic methods; curve fitting; information theory;
                   maximum likelihood estimates; statistical decision
                   theory; mathematical models; optimization; probability
                   distribution functions; regression analysis; signal
                   processing},
  year           = 1973
}

@Article{Andrec00,
  Author         = {Andrec, M. and Inman, K. G. and Weber, D. J. and Levy,
                   R. M. and Montelione, G. T.},
  Title          = {A {B}ayesian statistical method for the detection and
                   quantification of rotational diffusion anisotropy from
                   {NMR} relaxation data.},
  Journal        = jmr,
  Volume         = {146},
  Number         = {1},
  Pages          = {66-80},
  abstract       = {It has recently become more widely appreciated that
                   the presence of rotational diffusional anisotropy in
                   proteins and other macromolecules can have a
                   significant affect on the interpretation of NMR
                   relaxation data in terms of molecular motion. In this
                   paper, we show how commonly used NMR relaxation data
                   (R(1), R(2), and NOE) obtained at two spectrometer
                   frequencies can be analyzed using a Bayesian
                   statistical approach to reliably detect and quantify
                   the degree of rotational diffusion anisotropy. Our
                   approach differs from previous methods in that it does
                   not make assumptions concerning the internal motions
                   experienced by the residues which are used to quantify
                   the diffusion anisotropy, but rather averages the
                   results over all internal motions consistent with the
                   data. We demonstrate our method using synthetic data
                   corresponding to isotropic, axially symmetric
                   anisotropic, and fully asymmetric anisotropic
                   rotational diffusion, as well as experimental NMR data.
                   We compare the Bayesian statistical approach with a
                   widely used method for extracting tumbling parameters
                   using both synthetic and experimental data. While it
                   can be difficult to separate the effects of chemical
                   exchange from rotational anisotropy using this
                   "standard" method, these effects are readily separated
                   using Bayesian statistics. In addition, we find that
                   the Bayesian statistical approach requires considerably
                   less CPU time than an equivalent standard analysis.},
  authoraddress  = {Center for Advanced Biotechnology and Medicine,
                   Rutgers, Piscataway, New Jersey, 08855-0939, USA.},
  keywords       = {Algorithms ; Anisotropy ; *Bayes Theorem ; Computer
                   Simulation ; Diffusion ; Magnetic Resonance
                   Spectroscopy/*methods ; Monte Carlo Method ; Research
                   Support, Non-U.S. Gov't ; Research Support, U.S. Gov't,
                   P.H.S. ; Rotation},
  language       = {eng},
  doi            = {10.1006/jmre.2000.2113},
  medline-aid    = {10.1006/jmre.2000.2113 [doi] ; S109078070092113X [pii]},
  medline-ci     = {Copyright 2000 Academic Press.},
  medline-da     = {20001025},
  medline-dcom   = {20001025},
  medline-edat   = {2000/09/02 11:00},
  medline-fau    = {Andrec, M ; Inman, K G ; Weber, D J ; Levy, R M ;
                   Montelione, G T},
  medline-gr     = {GM-30580/GM/NIGMS ; GM-58888/GM/NIGMS ;
                   GM19856-02/GM/NIGMS ; etc.},
  medline-is     = {1090-7807},
  medline-jid    = {9707935},
  medline-lr     = {20041117},
  medline-mhda   = {2001/02/28 10:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {10968959},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-sb     = {IM},
  medline-so     = {J Magn Reson 2000 Sep;146(1):66-80.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=10968959},
  year           = 2000
}

@Article{Andrec99,
  Author         = {Andrec, M. and Montelione, G. T. and Levy, R. M.},
  Title          = {Estimation of dynamic parameters from {NMR} relaxation
                   data using the {L}ipari-{S}zabo model-free approach and
                   {B}ayesian statistical methods.},
  Journal        = jmr,
  Volume         = {139},
  Number         = {2},
  Pages          = {408-421},
  abstract       = {In order to analyze NMR relaxation data in terms of
                   parameters which describe internal motion, one must
                   first obtain a description of the overall tumbling of
                   the macromolecule in solution. Methods currently used
                   to estimate these global parameters may not always
                   provide reliable estimates of their values and
                   uncertainties. In this paper, we present a general data
                   analysis formalism based on products of Bayesian
                   marginal probability densities which can be used to
                   efficiently combine the information content from
                   multiple experiments, such as R(1), R(2), and NOE data
                   collected at multiple magnetic field strengths, or data
                   from cross-correlation or rotating frame relaxation
                   dispersion experiments. Our approach allows the
                   estimation of global tumbling and internal dynamical
                   parameters and their uncertainties without some of the
                   assumptions which are made in the commonly-used methods
                   for model-selection and global parameter estimation.
                   Compared to an equivalent classical statistical
                   approach, the Bayesian method not only is more
                   computationally efficient, but also provides greater
                   insight into the information content of the data. We
                   demonstrate that this approach can be used to estimate
                   both the isotropic rotational correlation time in the
                   context of the original and "extended" Lipari-Szabo
                   formalisms [Lipari \& Szabo, J. Am. Chem. Soc. 1982,
                   104, 4546; Clore et al., J. Am. Chem. Soc. 1990, 112,
                   4989], as well as the rotational diffusion coefficients
                   for axially symmetric anisotropic tumbling.},
  authoraddress  = {Wright-Rieman Laboratories, Rutgers, The State
                   University of New Jersey, Piscataway, New Jersey
                   08855-0939, USA.},
  keywords       = {Anisotropy ; Bayes Theorem ; Magnetic Resonance
                   Spectroscopy/*methods ; Monte Carlo Method ; Research
                   Support, Non-U.S. Gov't ; Research Support, U.S. Gov't,
                   P.H.S.},
  language       = {eng},
  doi            = {10.1006/jmre.1999.1839},
  medline-aid    = {10.1006/jmre.1999.1839 [doi] ; S1090780799918396 [pii]},
  medline-ci     = {Copyright 1999 Academic Press.},
  medline-da     = {20000316},
  medline-dcom   = {20000316},
  medline-edat   = {1999/07/29 10:00},
  medline-fau    = {Andrec, M ; Montelione, G T ; Levy, R M},
  medline-gr     = {GM-30580/GM/NIGMS ; GM-50733/GM/NIGMS},
  medline-is     = {1090-7807},
  medline-jid    = {9707935},
  medline-lr     = {20041117},
  medline-mhda   = {2000/03/18 09:00},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {10423379},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-sb     = {IM},
  medline-so     = {J Magn Reson 1999 Aug;139(2):408-21.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=10423379},
  year           = 1999
}

@Article{Baldisseri02,
  Author         = {Baldisseri, D.M. and Margolis, J.W. and Weber, D.J.
                   and Koo, J.H. and Margolis, F.L.},
  Title          = {Olfactory marker protein ({OMP}) exhibits a beta-clam
                   fold in solution: implications for target peptide
                   interaction and olfactory signal transduction.},
  Journal        = jmb,
  Volume         = {319},
  Number         = {3},
  Pages          = {823-837},
  abstract       = {Olfactory marker protein (OMP) is a ubiquitous,
                   cytoplasmic protein found in mature olfactory receptor
                   neurons of all vertebrates. Electrophysiological and
                   behavioral studies demonstrate that it is a modulator
                   of the olfactory signal transduction pathway. Here, we
                   demonstrate that the solution structure of OMP, as
                   determined by NMR studies, is a single globular domain
                   protein comprised of eight beta-strands forming two
                   beta-sheets oriented orthogonally to one another, thus
                   exhibiting a "beta-clam" or "beta-sandwich" fold:
                   beta-sheet 1 is comprised of beta3-beta8-beta1-beta2
                   and beta-sheet 2 contains beta6-beta5-beta4-beta7.
                   Insertions include two, long alpha-helices located on
                   opposite sides of the beta-clam and three flexible
                   loops. The juxtaposition of beta-strands
                   beta6-beta5-beta4-beta7-beta2-beta1-beta8-beta3 forms a
                   continuously curved surface and encloses one side of
                   the beta-clam. The "cleft" formed by the two
                   beta-sheets is opposite to the closed end of the
                   beta-clam. Using a peptide titration series, we have
                   identified this cleft as the binding surface for a
                   peptide derived from the Bex1 protein. The highly
                   conserved Omega-loop structure adjacent to the Bex1
                   peptide-binding surface found in OMP may be the site of
                   additional OMP-protein interactions related to its role
                   in modulating olfactory signal transduction. Thus, the
                   interaction between the OMP and Bex1 proteins could
                   facilitate the interaction between OMP and other
                   components of the olfactory signaling pathway.},
  authoraddress  = {Department of Biochemistry and Molecular Biology,
                   University of Maryland School of Medicine, 108 North
                   Greene Street, Baltimore, MD 21201-1503, USA
                   dbaldiss@umaryland.edu},
  keywords       = {Amino Acid Sequence ; Animals ; Conserved Sequence ;
                   Crystallography, X-Ray ; Hydrogen Bonding ; Models,
                   Molecular ; Molecular Sequence Data ; Nerve Tissue
                   Proteins/*chemistry/*metabolism ; Nuclear Magnetic
                   Resonance, Biomolecular ; Olfactory Marker Protein ;
                   Protein Binding ; Protein Folding ; Protein Structure,
                   Secondary ; Protein Structure, Tertiary ; Rats ;
                   Receptor Protein-Tyrosine Kinases/chemistry/metabolism
                   ; Receptor, EphB2 ; Research Support, U.S. Gov't,
                   Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S. ;
                   Sequence Alignment ; *Signal Transduction ;
                   Thermodynamics ; Titrimetry},
  language       = {eng},
  doi            = {10.1016/s0022-2836(02)00282-6},
  medline-aid    = {10.1016/S0022-2836(02)00282-6 [doi] ;
                   S0022-2836(02)00282-6 [pii]},
  medline-ci     = {(c) 2002 Elsevier Science Ltd.},
  medline-da     = {20020610},
  medline-dcom   = {20020710},
  medline-edat   = {2002/06/11 10:00},
  medline-fau    = {Baldisseri, Donna M ; Margolis, Joyce W ; Weber, David
                   J ; Koo, Jae Hyung ; Margolis, Frank L},
  medline-gr     = {DC 03112/DC/NIDCD ; DC 04752/DC/NIDCD ; RR
                   10441/RR/NCRR ; RR 15741/RR/NCRR},
  medline-is     = {0022-2836 (Print)},
  medline-jid    = {2985088R},
  medline-jt     = {Journal of molecular biology.},
  medline-lr     = {20051117},
  medline-mhda   = {2002/07/12 10:01},
  medline-own    = {NLM},
  medline-pl     = {England},
  medline-pmid   = {12054873},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Nerve Tissue Proteins) ; 0 (Olfactory Marker
                   Protein) ; 0 (Omp protein, rat) ; EC 2.7.1.112
                   (Receptor Protein-Tyrosine Kinases) ; EC 2.7.1.112
                   (Receptor, EphB2)},
  medline-sb     = {IM},
  medline-si     = {PDB/1JYT},
  medline-so     = {J Mol Biol. 2002 Jun 7;319(3):823-37.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=12054873},
  year           = 2002
}

@article{Baldwin2014,
  Author = {Baldwin, Andrew J.},
  Title = {{An exact solution for R2,eff in CPMG experiments in the case of two site chemical exchange}},
  Journal = jmr,
  issn = {10907807},
  Year = {2014},
  month = {Apr 14},
  doi = {10.1016/j.jmr.2014.02.023},
  Abstract = {The Carr-Purcell-Meiboom-Gill (CPMG) experiment is widely used to 
     quantitatively analyse the effects of chemical exchange on NMR spectra.
     In a CPMG experiment, the effective transverse relaxation rate, R2,eff, is typically 
     measured as a function of the pulse frequency, $\nu$CPMG. Here, an exact expression for 
     how R2,eff varies with $\nu$CPMG is derived for the commonly encountered scenario of 
     2-site chemical exchange of in-phase magnetisation. 
     This result, summarised in Appendix 1, generalises a frequently used equation derived 
     by Carver and Richards, published in 1972. The expression enables more rapid analysis of 
     CPMG data by both speeding up calculation of R2,eff over numerical methods by a factor 
     of ca. 130, and yielding exact derivatives for use in parameter optimisation. 
     Moreover, the derivation provides insight into the physical principles behind the experiment.},
  keywords       = {Magnetic Resonance Imaging ; Molecular Dynamics
                   Simulation ; *Nuclear Magnetic Resonance, Biomolecular ;
                   Programming Languages ; Protein Conformation ;
                   Proteins ; chemistry ; Software},

  keywords = {CPMG ; CPMG experiments ; Carver Richards Equation ; Chemical Exchange ; 
  			  Exact solution,Two-site exchange},
  url = {http://www.sciencedirect.com/science/article/pii/S1090780714000743}
}

@Article{Barbato92,
  Author         = {Barbato, G. and Ikura, M. and Kay, L. E. and Pastor,
                   R. W. and Bax, A.},
  Title          = {Backbone dynamics of calmodulin studied by 15{N}
                   relaxation using inverse detected two-dimensional {NMR}
                   spectroscopy: the central helix is flexible.},
  Journal        = biochem,
  Volume         = {31},
  Number         = {23},
  Pages          = {5269-5278},
  abstract       = {The backbone dynamics of Ca(2+)-saturated recombinant
                   Drosophila calmodulin has been studied by 15N
                   longitudinal and transverse relaxation experiments,
                   combined with 15N(1H) NOE measurements. Results
                   indicate a high degree of mobility near the middle of
                   the central helix of calmodulin, from residue K77
                   through S81, with order parameters (S2) in the 0.5-0.6
                   range. The anisotropy observed in the motion of the two
                   globular calmodulin domains is much smaller than
                   expected on the basis of hydrodynamic calculations for
                   a rigid dumbbell type structure. This indicates that,
                   for the purposes of 15N relaxation, the tumbling of the
                   N-terminal (L4-K77) and C-terminal (E82-S147) lobes of
                   calmodulin is effectively independent. A slightly
                   shorter motional correlation time (tau c approximately
                   6.3 ns) is obtained for the C-terminal domain compared
                   to the N-terminal domain (tau c approximately 7.1 ns),
                   in agreement with the smaller size of the C-terminal
                   domain. A high degree of mobility, with order
                   parameters of approximately 0.5, is also observed in
                   the loop that connects the first with the second
                   EF-hand type calcium binding domain and in the loop
                   connecting the third and fourth calcium binding domain.},
  authoraddress  = {Laboratory of Chemical Physics, National Institute of
                   Diabetes and Digestive and Kidney Diseases, National
                   Institutes of Health, Bethesda, Maryland 20892.},
  keywords       = {Animals ; Calmodulin/*chemistry/ultrastructure ;
                   Drosophila melanogaster ; Magnetic Resonance
                   Spectroscopy ; Motion ; Protein Conformation ;
                   Recombinant Proteins ; Research Support, U.S. Gov't,
                   P.H.S. ; Rotation},
  language       = {eng},
  medline-da     = {19920721},
  medline-dcom   = {19920721},
  medline-edat   = {1992/06/16},
  medline-fau    = {Barbato, G ; Ikura, M ; Kay, L E ; Pastor, R W ; Bax,
                   A},
  medline-is     = {0006-2960},
  medline-jid    = {0370623},
  medline-lr     = {20041117},
  medline-mhda   = {1992/06/16 00:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {1606151},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Calmodulin) ; 0 (Recombinant Proteins)},
  medline-sb     = {IM},
  medline-so     = {Biochemistry 1992 Jun 16;31(23):5269-78.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=1606151},
  year           = 1992,
  doi            = {10.1021/bi00138a005}
}

@Book{BellomoPreziosi94,
  Author         = {Bellomo, N. and Preziosi, L.},
  Title          = {Modelling Mathematical Methods and Scientific
                   Computation},
  Publisher      = {CRC Press},
  Series         = {CRC Mathematical Modelling Series},
  Address        = {Boca Raton, FL.},
  year           = 1994
}

@Article{Bieri11,
  Author = {Bieri, Michael and d'Auvergne, Edward and Gooley, Paul},
  Affiliation = {Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia},
  Title = {relax{GUI}: a new software for fast and simple {NMR} relaxation data analysis and calculation of ps-ns and $\mu$s motion of proteins},
  Journal = jbnmr,
  Publisher = {Springer Netherlands},
  issn = {0925-2738},
  keyword = {Physics and Astronomy},
  pages = {147-155},
  volume = {50},
  issue = {2},
  url = {http://dx.doi.org/10.1007/s10858-011-9509-1},
  doi = {10.1007/s10858-011-9509-1},
  abstract = {Investigation of protein dynamics on the ps-ns and μs-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was developed for fast and simple model-free analysis and is fully integrated into the software package relax. It is written in Python and uses wxPython to build the graphical user interface (GUI) for maximum performance and multi-platform use. This software allows the analysis of NMR relaxation data with ease and the generation of publication quality graphs as well as color coded images of molecular structures. The interface is designed for simple data analysis and management. The software was tested and validated against the command line version of relax.},
  year = {2011}
}
   
@Article{BieriGooley11,
  Author         = {Bieri, M. and Gooley, P. R.},
  Title          = {Automated {NMR} relaxation dispersion data analysis
                   using {NESSY}.},
  Journal        = {BMC Bioinformatics},
  Volume         = {12},
  Pages          = {421},
  abstract       = {BACKGROUND: Proteins are dynamic molecules with
                   motions ranging from picoseconds to longer than
                   seconds. Many protein functions, however, appear to
                   occur on the micro to millisecond timescale and
                   therefore there has been intense research of the
                   importance of these motions in catalysis and molecular
                   interactions. Nuclear Magnetic Resonance (NMR)
                   relaxation dispersion experiments are used to measure
                   motion of discrete nuclei within the micro to
                   millisecond timescale. Information about
                   conformational/chemical exchange, populations of
                   exchanging states and chemical shift differences are
                   extracted from these experiments. To ensure these
                   parameters are correctly extracted, accurate and
                   careful analysis of these experiments is necessary.
                   RESULTS: The software introduced in this article is
                   designed for the automatic analysis of relaxation
                   dispersion data and the extraction of the parameters
                   mentioned above. It is written in Python for multi
                   platform use and highest performance. Experimental data
                   can be fitted to different models using the
                   Levenberg-Marquardt minimization algorithm and
                   different statistical tests can be used to select the
                   best model. To demonstrate the functionality of this
                   program, synthetic data as well as NMR data were
                   analyzed. Analysis of these data including the
                   generation of plots and color coded structures can be
                   performed with minimal user intervention and using
                   standard procedures that are included in the program.
                   CONCLUSIONS: NESSY is easy to use open source software
                   to analyze NMR relaxation data. The robustness and
                   standard procedures are demonstrated in this article.},
  authoraddress  = {Department of Biochemistry and Molecular Biology,
                   Bio21 Molecular Science and Biotechnology Institute,
                   University of Melbourne, Parkville, Vic 3010,
                   Australia.},
  keywords       = {Magnetic Resonance Imaging ; Molecular Dynamics
                   Simulation ; *Nuclear Magnetic Resonance, Biomolecular
                   ; Programming Languages ; Protein Conformation ;
                   Proteins/*chemistry ; *Software},
  language       = {eng},
  medline-aid    = {1471-2105-12-421 [pii] ; 10.1186/1471-2105-12-421
                   [doi]},
  medline-crdt   = {2011/10/29 06:00},
  medline-da     = {20111115},
  medline-dcom   = {20120514},
  medline-dep    = {20111027},
  medline-edat   = {2011/10/29 06:00},
  medline-fau    = {Bieri, Michael ; Gooley, Paul R},
  medline-is     = {1471-2105 (Electronic) ; 1471-2105 (Linking)},
  medline-jid    = {100965194},
  medline-jt     = {BMC bioinformatics},
  medline-lid    = {10.1186/1471-2105-12-421 [doi]},
  medline-lr     = {20130627},
  medline-mhda   = {2012/05/15 06:00},
  medline-oid    = {NLM: PMC3215250},
  medline-own    = {NLM},
  medline-phst   = {2011/07/12 [received] ; 2011/10/27 [accepted] ;
                   2011/10/27 [aheadofprint]},
  medline-pl     = {England},
  medline-pmc    = {PMC3215250},
  medline-pmid   = {22032230},
  medline-pst    = {epublish},
  medline-pt     = {Journal Article ; Research Support, Non-U.S. Gov't},
  medline-rn     = {0 (Proteins)},
  medline-sb     = {IM},
  medline-so     = {BMC Bioinformatics. 2011 Oct 27;12:421. doi:
                   10.1186/1471-2105-12-421.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=22032230},
  doi            = {10.1186/1471-2105-12-421},
  year           = 2011
}

@Article{Blackledge98,
  Author         = {Blackledge, M. and Cordier, F. and Dosset, P. and
                   Marion, D.},
  Title          = {Precision and uncertainty in the characterization of
                   anisotropic rotational diffusion by {N}-15 relaxation},
  Journal        = jacs,
  Volume         = {120},
  Number         = {18},
  Pages          = {4538-4539},
  address        = {1155 16TH ST, NW, Washington, DC 20036 USA},
  authoraddress  = {CEA, Jean Pierre Ebel CNRS, Inst Biol Struct, F-38027
                   Grenoble, France.},
  citedref       = {ABRAGAM A, 1961, PRINCIPLES NUCL MAGN ; BARBATO G,
                   1992, BIOCHEMISTRY-US, V31, P5269 ; BROADHURST RW,
                   1995, BIOCHEMISTRY-US, V34, P16608 ; BRUSCHWEILER R,
                   1995, SCIENCE, V268, P886 ; CLORE GM, 1990, J AM CHEM
                   SOC, V112, P4989 ; CORDIER F, UNPUB ; FARROW NA, 1994,
                   BIOCHEMISTRY-US, V33, P5984 ; HANSEN AP, 1994,
                   BIOCHEMISTRY-US, V33, P15418 ; KORDEL J, 1992,
                   BIOCHEMISTRY-US, V31, P4856 ; LEE LK, 1997, J BIOMOL
                   NMR, V9, P287 ; LIPARI G, 1982, J AM CHEM SOC, V104,
                   P4546 ; LIPARI G, 1982, J AM CHEM SOC, V104, P4559 ;
                   LUGINBUHL P, 1997, BIOCHEMISTRY-US, V36, P7305 ; MACKAY
                   JP, 1996, BIOCHEMISTRY-US, V35, P4867 ; METROPOLIS N,
                   1953, J CHEM PHYS, V21, P1087 ; PENG JW, 1992, J MAGN
                   RESON, V98, P308 ; TJANDRA N, 1995, EUR J BIOCHEM,
                   V230, P1014 ; TJANDRA N, 1995, J AM CHEM SOC, V117,
                   P12562 ; TJANDRA N, 1996, J BIOMOL NMR, V8, P273 ;
                   TJANDRA N, 1997, NAT STRUCT BIOL, V4, P443 ; WOESSNER
                   DE, 1962, J CHEM PHYS, V37, P647 ; ZHENG Z, 1995,
                   BIOCHEMISTRY-US, V34, P5212},
  isifile-dt     = {Article},
  isifile-ga     = {ZN435},
  isifile-j9     = {J Amer Chem Soc},
  isifile-ji     = {J. Am. Chem. Soc.},
  isifile-nr     = {22},
  isifile-pi     = {Washington},
  isifile-rp     = {Blackledge, M, CEA, Jean Pierre Ebel CNRS, Inst Biol
                   Struct, 41 Ave ; Martyrs, F-38027 Grenoble, France.},
  isifile-sc     = {Chemistry, Multidisciplinary},
  isifile-tc     = {45},
  issn           = {0002-7863},
  keywords       = {[ISI:] model-free approach; magnetic-resonance
                   relaxation; backbone dynamics; nmr relaxation;
                   spectroscopy; macromolecules; protein; domain; range ;;},
  language       = {English},
  month          = {May 13},
  publisher      = {Amer Chemical Soc},
  size           = {2 p.},
  sourceid       = {ISI:000073645600043},
  year           = 1998
}

@Article{Bloch46,
  Author         = {Bloch, F.},
  Title          = {Nuclear induction},
  Journal        = physrev,
  Volume         = {70},
  Number         = {7-8},
  Pages          = {460-474},
  address        = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
  doc-delivery-number = {UB265},
  doi            = {10.1103/PhysRev.70.460},
  issn           = {0031-899X},
  language       = {English},
  number-of-cited-references = {14},
  publisher      = {AMERICAN PHYSICAL SOC},
  research-areas = {Physics},
  times-cited    = {2053},
  type           = {Article},
  unique-id      = {ISI:A1946UB26500003},
  web-of-science-categories = {Physics, Multidisciplinary},
  year           = 1946
}

@Article{Bloembergen48,
  Author         = {Bloembergen, N. and Purcell, E. M. and Pound, R. V.},
  Title          = {Relaxation effects in nuclear magnetic resonance
                   absorption},
  Journal        = physrev,
  Volume         = {73},
  Number         = {7},
  Pages          = {679-712},
  address        = {One Physics Ellipse, College PK, MD 20740-3844 USA},
  citedref       = {ALPERT NL, 1947, PHYS REV, V72, P637 ; BITTER F, 1947,
                   PHYS REV, V71, P738 ; BLOCH F, 1946, PHYS REV, V70,
                   P460 ; BLOCH F, 1946, PHYS REV, V70, P474 ; BROER LJF,
                   1943, PHYSICA, V10, P801 ; BROER LJF, 1945, THESIS
                   AMSTERDAM, P56 ; CUMMEROW RL, 1947, PHYS REV, V72,
                   P1233 ; DEBYE P, 1945, POLAR MOL, CH5 ; DICKE RH, 1946,
                   REV SCI INSTRUM, V17, P268 ; FRIIS HT, 1944, P IRE,
                   V32, P419 ; GORTER CJ, 1942, PHYSICA, V9, P591 ; GORTER
                   GJ, 1947, PARAMAGNETIC RELAXAT, P4 ; HEITLER W, 1936, P
                   ROY SOC LOND A MAT, V155, P629 ; KELLOGG JMB, 1940,
                   PHYS REV, V57, P677 ; PAKE GE, J CHEM PHYS ; PAULING L,
                   1940, NATURE CHEM BOND, P302 ; PURCELL EM, 1946, PHYS
                   REV, V69, P37 ; PURCELL EM, 1946, PHYS REV, V69, P681 ;
                   PURCELL EM, 1946, PHYS REV, V70, P986 ; PURCELL EM,
                   1946, PHYS REV, V70, P988 ; ROLLIN BV, 1946, NATURE,
                   V158, P669 ; ROLLIN BV, 1947, NATURE LOND, V160, P457 ;
                   ROLLIN BV, 1947, NATURE, V159, P201 ; ROSE ME, 1938,
                   PHYS REV, V53, P715 ; SAXTON JA, 1945, C115 RAD RES
                   BOARD R ; TORREY HC, COMMUNICATION ; VALLEY GE, VACUUM
                   TUBE AMPLIFIE, V18 ; VANVLECK JH, PHYS REV ; VANVLECK
                   JH, 1932, ELECTRIC MAGNETIC SU, CH11 ; WALLER I, 1932,
                   Z PHYS, V79, P370 ; WANG MC, 1945, REV MOD PHYS, V17,
                   P323 ; WEISSKOPF V, 1930, Z PHYS, V63, P54 ; WEISSKOPF
                   V, 1930, Z PHYS, V65, P18 ; ZAVOISKY E, 1945, J PHYS
                   USSR, V9, P211},
  isifile-dt     = {Article},
  isifile-ga     = {UB298},
  isifile-j9     = {Phys Rev},
  isifile-nr     = {34},
  isifile-pi     = {College PK},
  isifile-sc     = {Physics, Multidisciplinary},
  isifile-tc     = {3697},
  issn           = {0031-899X},
  language       = {English},
  publisher      = {American Physical Soc},
  size           = {34 p.},
  sourceid       = {ISI:A1948UB29800004},
  year           = 1948,
  doi            = {10.1103/PhysRev.73.679}
}

@Article{Bracken99,
  Author         = {Bracken, C. and Carr, P.A. and Cavanagh, J. and
                   Palmer, 3rd, A.G.},
  Title          = {Temperature dependence of intramolecular dynamics of
                   the basic leucine zipper of {GCN}4: implications for
                   the entropy of association with {DNA}.},
  Journal        = jmb,
  Volume         = {285},
  Number         = {5},
  Pages          = {2133-2146},
  abstract       = {The basic leucine zipper domain of the yeast
                   transcription factor GCN4 consists of a C-terminal
                   leucine zipper and an N-terminal basic DNA-binding
                   region that achieves a stable structure only after
                   association with DNA. Backbone dynamics of a peptide
                   encompassing the basic and leucine zipper bZip domain
                   (residues 226-281) are described using NMR
                   spectroscopy. The 15N longitudinal relaxation rates,
                   15N transverse relaxation rates, and inverted question
                   mark1H inverted question mark-15N nuclear Overhauser
                   effects were measured for the backbone amide nitrogen
                   atoms at 290 K, 300 K, and 310 K. The relaxation data
                   were interpreted using reduced spectral density mapping
                   to determine values of the spectral density function,
                   J(omega), at the frequencies 0, omegaN, and 0.87omegaH
                   to characterize overall and intramolecular motions on
                   picosecond-nanosecond timescales. To account for the
                   temperature dependence of overall rotational diffusion,
                   the J(0) values were normalized using Stoke's Law. At
                   310 K, the 13Calpha and 13CO chemical shifts in
                   conjunction with the spectral density values indicate
                   that the leucine zipper sequence forms a highly ordered
                   alpha-helix, while the basic region populates an
                   ensemble of highly dynamic transient structures with
                   substantial helical character. The normalized values of
                   J(0) and the values of J(0.87omegaH) for residues in
                   the leucine zipper dimerization domain are independent
                   of temperature. In contrast, residues in the basic
                   region exhibit pronounced increases in the normalized
                   J(0) and decreases in J(0.87omegaH) as temperature is
                   decreased. A strong correlation exists between the
                   temperature dependence of 13CO chemical shifts and of
                   J(0.87omegaH). These results suggest that, for the
                   basic region, lowering the temperature increases the
                   population of transient helical conformations, and
                   concomitantly reduces the amplitude or timescale of
                   conformational fluctuations on picosecond-nanosecond
                   timescales. Changes in the conformational dynamics of
                   the peptide backbone of the basic region that accompany
                   DNA binding contribute to the overall thermodynamics of
                   complex formation. The change in backbone
                   conformational entropy derived from NMR spin-relaxation
                   data agrees well with the result calculated from
                   calorimetric measurements. Restriction of the
                   conformational space accessible to the basic region may
                   significantly reduce the entropic cost associated with
                   formation of the basic region helices consequent to DNA
                   binding.},
  authoraddress  = {Department of Biochemistry and Molecular Biophysics,
                   Columbia University, 630 West 168th Street, New York,
                   NY, 10032, USA.},
  keywords       = {Amino Acid Sequence ; Circular Dichroism ;
                   DNA/chemistry/*metabolism ; DNA-Binding
                   Proteins/*chemistry/metabolism ; Entropy ; Fungal
                   Proteins/*chemistry/metabolism ; *Leucine Zippers ;
                   Magnetic Resonance Spectroscopy/methods ; Models,
                   Molecular ; Molecular Sequence Data ; Protein
                   Conformation ; Protein Kinases/*chemistry/metabolism ;
                   Research Support, Non-U.S. Gov't ; Research Support,
                   U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't,
                   P.H.S. ; *Saccharomyces cerevisiae Proteins ;
                   Temperature},
  language       = {eng},
  doi            = {s0022-2836(98)92429-9},
  medline-aid    = {S0022-2836(98)92429-9 [pii] ; 10.1006/jmbi.1998.2429
                   [doi]},
  medline-ci     = {Copyright 1999 Academic Press Limited.},
  medline-da     = {19990325},
  medline-dcom   = {19990325},
  medline-edat   = {1999/02/02 03:01},
  medline-fau    = {Bracken, C ; Carr, P A ; Cavanagh, J ; Palmer, A G 3rd},
  medline-gr     = {GM-17562/GM/NIGMS},
  medline-is     = {0022-2836 (Print)},
  medline-jid    = {2985088R},
  medline-jt     = {Journal of molecular biology.},
  medline-lr     = {20051121},
  medline-mhda   = {2001/03/28 10:01},
  medline-own    = {NLM},
  medline-pl     = {ENGLAND},
  medline-pmid   = {9925790},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (DNA-Binding Proteins) ; 0 (Fungal Proteins) ; 0
                   (Saccharomyces cerevisiae Proteins) ; 9007-49-2 (DNA) ;
                   EC 2.7.1.37 (Protein Kinases)},
  medline-sb     = {IM},
  medline-so     = {J Mol Biol. 1999 Feb 5;285(5):2133-46.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=9925790},
  year           = 1999
}

@Article{Broyden70,
  Author         = {Broyden, C. G.},
  Title          = {The Convergence of a Class of Double-rank
                   Minimization Algorithms 1. {G}eneral
                   Considerations},
  Journal        = jima,
  Volume         = {6},
  Number         = {1},
  Pages          = {76-90},
  abstract       = {This paper presents a more detailed analysis of a
                   class of minimization algorithms, which includes as a
                   special case the DFP (Davidon-Fletcher-Powell) method,
                   than has previously appeared. Only quadratic functions
                   are considered but particular attention is paid to the
                   magnitude of successive errors and their dependence
                   upon the initial matrix. On the basis of this a
                   possible explanation of some of the observed
                   characteristics of the class is tentatively suggested. },
  doi            = {10.1093/imamat/6.1.76},
  eprint         = {http://imamat.oxfordjournals.org/cgi/reprint/6/1/76.pdf},
  url            = {http://imamat.oxfordjournals.org/cgi/content/abstract/6/1/76},
  year           = 1970
}

@Article{Bruschweiler95,
  Author         = {Br{\"u}schweiler, R. and Liao, X. and Wright, P. E.},
  Title          = {Long-range motional restrictions in a multidomain
                   zinc-finger protein from anisotropic tumbling.},
  Journal        = sci,
  Volume         = {268},
  Number         = {5212},
  Pages          = {886-889},
  abstract       = {Structural characterization of biomolecules in
                   solution by nuclear magnetic resonance (NMR)
                   spectroscopy is based primarily on the use of
                   interproton distances derived from homonuclear
                   cross-relaxation experiments. Information about short
                   time-scale dynamics, on the other hand, is obtained
                   from relaxation rates of heteronuclear spin pairs such
                   as 15N-1H. By combining the two types of data and
                   utilizing the dependence of heteronuclear NMR
                   relaxation rates on anisotropic diffusional rotational
                   tumbling, it is possible to obtain structural
                   information about long-range motional correlations
                   between protein domains. This approach was applied to
                   characterize the relative orientations and mobilities
                   of the first three zinc-finger domains of the Xenopus
                   transcription factor TFIIIA in aqueous solution. The
                   data indicate that the motions of the individual
                   zinc-finger domains are highly correlated on time
                   scales shorter than 10 nanoseconds and that the average
                   conformation of the three-finger polypeptide is
                   elongated.},
  authoraddress  = {Laboratorium fur Physikalische Chemie, Eidgenossiche
                   Technische Hochschule Zentrum, Zurich, Switzerland.},
  keywords       = {Anisotropy ; DNA-Binding Proteins/*chemistry ;
                   Magnetic Resonance Spectroscopy ; Mathematics ; Models,
                   Molecular ; Protein Conformation ; Proteins/chemistry ;
                   Research Support, Non-U.S. Gov't ; Research Support,
                   U.S. Gov't, P.H.S. ; Solutions ; Transcription Factor
                   TFIIIA ; Transcription Factors/*chemistry ; *Zinc
                   Fingers},
  language       = {eng},
  medline-da     = {19950616},
  medline-dcom   = {19950616},
  medline-edat   = {1995/05/12},
  medline-fau    = {Bruschweiler, R ; Liao, X ; Wright, P E},
  medline-gr     = {GM 36643/GM/NIGMS},
  medline-is     = {0036-8075},
  medline-jid    = {0404511},
  medline-lr     = {20041117},
  medline-mhda   = {1995/05/12 00:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {7754375},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (DNA-Binding Proteins) ; 0 (Proteins) ; 0
                   (Solutions) ; 0 (Transcription Factor TFIIIA) ; 0
                   (Transcription Factors) ; 0 (ZF-1 protein, Sus scrofa)},
  medline-sb     = {IM},
  medline-so     = {Science 1995 May 12;268(5212):886-9.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=7754375},
  year           = 1995,
  doi            = {10.1126/science.7754375}
}

@Book{BurnhamAnderson98,
  Author         = {Burnham, Kenneth P. and Anderson, David Raymond},
  Title          = {Model selection and inference: {A} practical
                   information-theoretic approach},
  Publisher      = {Springer-Verlag},
  Address        = {New York},
  description    = {This book is unique in that it covers the philosophy
                   of model-based data analysis and a strategy for the
                   analysis of empirical data. Model selection, under the
                   information theoretic approach presented here, attempts
                   to identify the (likely) best model, orders the models
                   from best to worst, and measures the plausibility
                   ("calibration") that each model is really the best as
                   an inference. Model selection methods are extended to
                   allow inference from more than a single "best" model.
                   Several methods are given that allow the uncertainty as
                   to which model is "best" to be incorporated into
                   estimates of precision. An array of examples are given
                   to illustrate various technical issues. This is an
                   applied book written primarily for biologists and
                   statisticians using models for making inferences from
                   empirical data. Research biologists working either in
                   the field or in the laboratory will find simple methods
                   that are likely to be useful in their investigations.
                   Applied statisticians will find the information
                   theoretic methods presented here quite useful and a
                   superior alternative, especially for observational
                   studies. People interested in the empirical sciences
                   will find this material useful as it offers an
                   alternative to hypothesis testing and Bayesian
                   approaches.},
  isbn           = {0387985042},
  pages          = {320},
  year           = 1998
}

@Book{Cavanagh95,
  Author         = {Cavanagh, John and Fairbrother, Wayne J. and Palmer,
                   3rd, Arthur G. and Skelton, Nicholas J.},
  Title          = {Protein {NMR} {S}pectroscopy : {P}rinciples and
                   {P}ractice},
  Publisher      = {Academic Press},
  Edition        = {1st},
  contents       = {Classical NMR Spectroscopy. Theoretical Description of
                   NMR Spectroscopy. Experimental Aspects of NMR
                   Spectroscopy. Multi-Dimensional NMR Spectroscopy.
                   Relaxation and Dynamic Processes. Experimental 1H NMR
                   Methods. Heteronuclear NMR Experiments. Sequential
                   Assignments and Structure Calculations. Chapter
                   References. Subject Index.},
  description    = {Protein NMR Spectroscopy: Principles and Practice
                   combines a comprehensive theoretical treatment of high
                   resolution NMR spectroscopy with an extensive
                   exposition of the experimental techniques applicable to
                   proteins and other biological macromolecules. Beginning
                   with simple theoretical models and experimental
                   techniques, Protein NMR Spectroscopy: Principles and
                   Practice develops the complete repertoire of
                   theoretical principals and experimental practices
                   necessary for understanding and implementing the most
                   sophisticated NMR experiments. Protein NMR
                   Spectroscopy: Principles and Practice is written as a
                   graduate-level textbook and will be of particular
                   interest to biochemists, chemists, biophysicists, and
                   structural biologists who utilize NMR spectroscopy as a
                   research tool or who wish to remain abreast of the
                   latest developments in this increasingly important
                   area.},
  features-and-benefits = {Special Features: First book to combine detailed NMR
                   theory discussions with experimental applications to
                   biomolecules. All the theory required to understand
                   these experiments and others. Easy to follow
                   progression from a fundamental level to an advanced
                   level. Theory of NMR and practical applications for
                   biomolecular investigations presented. Theory applied
                   to very practical situations. Comprehensive treatment
                   of different "levels" of theory from simple ideas to
                   density matrix analysis and operator practices.
                   Comprehensive description of multi dimensional NMR
                   experiments as applied to unlabeled, 15N-labeled and
                   doubly (13C/15N) labeled proteins.},
  isbn           = {0-12-164490-1},
  measurements   = {152 X 229 mm},
  month          = {28 } # nov,
  pages          = {587},
  year           = 1995
}

@Article{Butterwick04,
  Author         = {Butterwick, Joel A. and Loria, Patrick J. and Astrof,
                   Nathan S. and Kroenke, Christopher D. and Cole, Roger and Rance, Mark and
                   Palmer, 3rd, Arthur G.},
  Title          = {Multiple time scale backbone dynamics of homologous
                   thermophilic and mesophilic ribonuclease {HI} enzymes.},
  Journal        = jmb,
  Volume         = {339},
  Number         = {4},
  Pages          = {855-871},
  abstract       = {Backbone conformational fluctuations on multiple time
                   scales in a cysteine-free Thermus thermophilus
                   ribonuclease HI mutant (ttRNH(*)) are quantified using
                   (15)N nuclear magnetic spin relaxation.
                   Laboratory-frame relaxation data acquired at 310 K and
                   at static magnetic field strengths of 11.7, 14.1 and
                   18.8 T are analysed using reduced spectral density
                   mapping and model-free approaches. Chemical exchange
                   line broadening is characterized using Hahn-echo
                   transverse and multiple quantum relaxation data
                   acquired over a temperature range of 290-320 K and at a
                   static magnetic field strength of 14.1 T. Results for
                   ttRNH(*) are compared to previously published data for
                   a mesophilic homologue, Escherichia coli ribonuclease
                   HI (ecRNH). Intramolecular conformational fluctuations
                   on the picosecond-to-nanosecond time scale generally
                   are similar for ttRNH(*) and ecRNH. beta-Strands 3 and
                   5 and the glycine-rich region are more rigid while the
                   substrate-binding handle region and C-terminal tail are
                   more flexible in ttRNH(*) than in ecRNH. Rigidity in
                   the two beta-strands and the glycine-rich region,
                   located along the periphery of the central beta-sheet,
                   may be associated with the increased thermodynamic
                   stability of the thermophilic enzyme. Chemical exchange
                   line broadening, reflecting microsecond-to-millisecond
                   time scale conformational changes, is more pronounced
                   in ttRNH(*) than in ecRNH, particularly for residues in
                   the handle and surrounding the catalytic site. The
                   temperature dependence of chemical exchange show an
                   increase of approximately 15 kJ/mol in the apparent
                   activation energies for ttRNH(*) residues in the handle
                   compared to ecRNH. Increased activation barriers,
                   coupled with motion between alpha-helices B and C not
                   present in ecRNH, may be associated with the reduced
                   catalytic activity of the thermophilic enzyme at 310 K.},
  authoraddress  = {Department of Biochemistry and Molecular Biophysics,
                   Columbia University, 630 West 168th Street, Box 36, New
                   York, NY 10032-3702, USA.},
  keywords       = {Amino Acid Sequence ; Models, Molecular ; Molecular
                   Sequence Data ; Nuclear Magnetic Resonance,
                   Biomolecular ; Protein Conformation ; Research Support,
                   U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't,
                   P.H.S. ; Ribonuclease H, Calf
                   Thymus/chemistry/*metabolism ; Sequence Homology, Amino
                   Acid ; Thermus thermophilus/enzymology},
  language       = {eng},
  doi            = {10.1016/j.jmb.2004.03.055},
  medline-aid    = {10.1016/j.jmb.2004.03.055 [doi] ; S0022283604003572
                   [pii]},
  medline-da     = {20040528},
  medline-dcom   = {20040713},
  medline-edat   = {2004/05/29 05:00},
  medline-fau    = {Butterwick, Joel A ; Patrick Loria, J ; Astrof, Nathan
                   S ; Kroenke, Christopher D ; Cole, Roger ; Rance, Mark
                   ; Palmer, Arthur G 3rd},
  medline-gr     = {GM08281/GM/NIGMS ; GM40089/GM/NIGMS ; GM50291/GM/NIGMS
                   ; GM66354/GM/NIGMS},
  medline-is     = {0022-2836 (Print)},
  medline-jid    = {2985088R},
  medline-jt     = {Journal of molecular biology.},
  medline-lr     = {20041117},
  medline-mhda   = {2004/07/14 05:00},
  medline-own    = {NLM},
  medline-phst   = {2004/01/30 [received] ; 2004/03/15 [revised] ;
                   2004/03/22 [accepted]},
  medline-pl     = {England},
  medline-pmid   = {15165855},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {EC 3.1.26.4 (Ribonuclease H, Calf Thymus) ; EC
                   3.1.26.4 (ribonuclease HI)},
  medline-sb     = {IM},
  medline-so     = {J Mol Biol. 2004 Jun 11;339(4):855-71.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=15165855},
  year           = 2004
}

@Article{CarverRichards72,
  Author         = {Carver, J.P. and Richards, R.E.},
  Title          = {General 2-site solution for chemical exchange
                   produced dependence of {T2} upon {C}arr-{P}urcell pulse
                   separation},
  Journal        = jmr,
  Volume         = {6},
  Number         = {1},
  Pages          = {89-105},
  address        = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495},
  doc-delivery-number = {L5576},
  doi            = {10.1016/0022-2364(72)90090-X},
  issn           = {1090-7807},
  journal-iso    = {J. Magn. Reson.},
  language       = {English},
  number-of-cited-references = {13},
  publisher      = {ACADEMIC PRESS INC},
  research-areas = {Biochemistry \& Molecular Biology; Physics;
                   Spectroscopy},
  times-cited    = {224},
  type           = {Article},
  unique-id      = {ISI:A1972L557600008},
  web-of-science-categories = {Biochemical Research Methods; Physics, Atomic,
                   Molecular \& Chemical; Spectroscopy},
  year           = 1972
}

@Article{Chen04,
  Author         = {Chen, J. and Brooks, 3rd, C. L. and Wright, P. E.},
  Title          = {Model-free analysis of protein dynamics: assessment of
                   accuracy and model selection protocols based on
                   molecular dynamics simulation.},
  Journal        = jbnmr,
  Volume         = {29},
  Number         = {3},
  Pages          = {243-257},
  abstract       = {The popular model-free approach to analyze NMR
                   relaxation measurements has been examined using
                   artificial amide (15)N relaxation data sets generated
                   from a 10 nanosecond molecular dynamics trajectory of a
                   dihydrofolate reductase ternary complex in explicit
                   water. With access to a detailed picture of the
                   underlying internal motions, the efficacy of model-free
                   analysis and impact of model selection protocols on the
                   interpretation of NMR data can be studied. In the limit
                   of uncorrelated global tumbling and internal motions,
                   fitting the relaxation data to the model-free models
                   can recover a significant amount of quantitative
                   information on the internal dynamics. Despite a slight
                   overestimation, the generalized order parameter is
                   quite accurately determined. However, the model-free
                   analysis appears to be insensitive to the presence of
                   nanosecond time scale motions with relatively small
                   magnitude. For such cases, the effective correlation
                   time can be significantly underestimated. As a result,
                   proteins appear to be more rigid than they really are.
                   The model selection protocols have a major impact on
                   the information one can reliably obtain. The commonly
                   employed protocol based on step-up hypothesis testing
                   has severe drawbacks of oversimplification and
                   underfitting. The consequences are that the order
                   parameter is more severely overestimated and the
                   correlation time more severely underestimated. Instead,
                   model selection based on Bayesian Information Criteria
                   (BIC), recently introduced to the model-free analysis
                   by d'Auvergne and Gooley (2003), provides a better
                   balance between bias and variance. More appropriate
                   models can be selected, leading to improved estimate of
                   both the order parameter and correlation time. In
                   addition, the computational cost is significantly
                   reduced and subjective parameters such as the
                   significance level are unnecessary.},
  authoraddress  = {Department of Molecular Biology, The Scripps Research
                   Institute, 10550 North Torrey Pines Road, La Jolla, CA
                   92037, USA.},
  keywords       = {Anisotropy ; Bayes Theorem ; Escherichia
                   coli/enzymology ; Magnetic Resonance
                   Spectroscopy/*methods ; Models, Statistical ; Models,
                   Theoretical ; Nitrogen/chemistry ; Protein Folding ;
                   Proteins/*chemistry ; Research Support, Non-U.S. Gov't
                   ; Research Support, U.S. Gov't, P.H.S. ; Software ;
                   Tetrahydrofolate Dehydrogenase/chemistry ; Time Factors},
  language       = {eng},
  doi            = {10.1023/b:jnmr.0000032504.70912.58},
  medline-aid    = {10.1023/B:JNMR.0000032504.70912.58 [doi] ; 5266056
                   [pii]},
  medline-da     = {20040623},
  medline-dcom   = {20050131},
  medline-edat   = {2004/06/24 05:00},
  medline-fau    = {Chen, Jianhan ; Brooks, Charles L 3rd ; Wright, Peter
                   E},
  medline-gr     = {GM48807/GM/NIGMS ; GM56879/GM/NIGMS},
  medline-is     = {0925-2738},
  medline-jid    = {9110829},
  medline-mhda   = {2005/02/03 09:00},
  medline-own    = {NLM},
  medline-pl     = {Netherlands},
  medline-pmid   = {15213423},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Proteins) ; 7727-37-9 (Nitrogen) ; EC 1.5.1.3
                   (Tetrahydrofolate Dehydrogenase)},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR 2004 Jul;29(3):243-57.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=15213423},
  year           = 2004
}

@Article{Clore90b,
  Author         = {Clore, G. M. and Driscoll, P. C. and Wingfield, P. T.
                   and Gronenborn, A. M.},
  Title          = {Analysis of the backbone dynamics of interleukin-1
                   beta using two-dimensional inverse detected
                   heteronuclear 15{N}-1{H} {NMR} spectroscopy.},
  Journal        = biochem,
  Volume         = {29},
  Number         = {32},
  Pages          = {7387-7401},
  abstract       = {The backbone dynamics of uniformly 15N-labeled
                   interleukin-1 beta are investigated by using
                   two-dimensional inverse detected heteronuclear 15N-1H
                   NMR spectroscopy. 15N T1, T2, and NOE data at a
                   spectrometer frequency of 600 MHz are obtained for 90\%
                   of the backbone amide groups. The data provide evidence
                   for motions on three time scales. All the residues
                   exhibit very fast motions on a time scale of
                   approximately less than 20-50 ps that can be
                   characterized by a single-order parameter with an
                   average value of 0.82 +/- 0.05. For a model comprising
                   free diffusion within a cone, these residue-specific
                   order parameters translate to an average cone semiangle
                   of 20.7 +/- 3.3 degrees. Thirty-two residues also
                   display motions on a time scale of 0.5-4 ns, slightly
                   less than the overall rotational correlation time of
                   the protein (8.3 ns). These additional motions must be
                   invoked to account for the discrepancy between
                   experiment and the simplest theoretical formulation in
                   which the internal motions are described by only two
                   parameters, a generalized order parameter and an
                   effective correlation time [Lipari, G., \& Szabo, A.
                   (1982a) J. Am. Chem. Soc. 104, 4546-4559]. In
                   particular, while the simple formulation can account
                   for the 15N T1 and T2 data, it fails to account for the
                   15N-1H NOE data and yields calculated values for the
                   NOEs that are either too small or negative, whereas the
                   observed NOEs are positive. With the introduction of
                   two internal motions that are faster than the
                   rotational correlation time and differ in time scales
                   by at least 1-2 orders of magnitude [Clore, G. M.,
                   Szabo, A., Bax, A., Kay, L. E., Driscoll, P. C., \&
                   Gronenborn, A. M. (1990) J. Am. Chem. Soc. 112,
                   4989-4991], all the relaxation data for these 32
                   residues can be fitted by two order parameters and an
                   effective correlation time for the slower of the two
                   internal motions. A simple model for these two motions
                   is one in which the very fast motion involves axially
                   symmetric diffusion within a cone, while the slower
                   motion comprises jumps between two different
                   orientations of the NH vector. For such a model the
                   jump angle (excluding the C-terminal residue) ranges
                   from 15 degrees to 69 degrees with a mean value of 28.6
                   +/- 14.0 degrees. Another 42 residues are characterized
                   by some sort of motion on the 30-ns-10-ms time scale,
                   which results in 15N line broadening due to chemical
                   exchange between different conformational substates
                   with distinct 15N chemical shifts.(ABSTRACT TRUNCATED
                   AT 400 WORDS)},
  authoraddress  = {Laboratory of Chemical Physics, National Institute of
                   Diabetes and Digestive and Kidney Diseases, National
                   Institutes of Health, Bethesda, Maryland 20892.},
  keywords       = {Amino Acid Sequence ; Hydrogen ; *Interleukin-1 ;
                   Kinetics ; Magnetic Resonance Spectroscopy ; Molecular
                   Sequence Data ; Nitrogen Isotopes ; Protein
                   Conformation ; Research Support, U.S. Gov't, P.H.S. ;
                   Structure-Activity Relationship ; X-Ray Diffraction},
  language       = {eng},
  medline-da     = {19901205},
  medline-dcom   = {19901205},
  medline-edat   = {1990/08/14},
  medline-ein    = {Biochemistry 1991 Jan 8;30(1):312},
  medline-fau    = {Clore, G M ; Driscoll, P C ; Wingfield, P T ;
                   Gronenborn, A M},
  medline-is     = {0006-2960},
  medline-jid    = {0370623},
  medline-lr     = {20041117},
  medline-mhda   = {1990/08/14 00:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {2223770},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Interleukin-1) ; 0 (Nitrogen Isotopes) ; 1333-74-0
                   (Hydrogen)},
  medline-sb     = {IM},
  medline-so     = {Biochemistry 1990 Aug 14;29(32):7387-401.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=2223770},
  year           = 1990
}

@Article{Clore90a,
  Author         = {Clore, G. M. and Szabo, A. and Bax, A. and Kay, L. E.
                   and Driscoll, P. C. and Gronenborn, A. M.},
  Title          = {Deviations from the simple 2-parameter model-free
                   approach to the interpretation of {N}-15 nuclear
                   magnetic-relaxation of proteins},
  Journal        = jacs,
  Volume         = {112},
  Number         = {12},
  Pages          = {4989-4991},
  address        = {1155 16th St, NW, Washington, DC 20036},
  citedref       = {ABRAGAM A, 1961, PRINCIPLES NUCLEAR M ; CLORE GM, IN
                   PRESS BIOCHEMISTR ; DELLWO MJ, 1989, J AM CHEM SOC,
                   V111, P4571 ; KARPLUS M, 1981, CRC CRIT REV BIOCH, V9,
                   P293 ; KAY LE, 1989, BIOCHEMISTRY-US, V28, P8972 ; LEVY
                   RM, 1981, J AM CHEM SOC, V103, P994 ; LIPARI G, 1982, J
                   AM CHEM SOC, V104, P4546 ; LIPARI G, 1982, J AM CHEM
                   SOC, V104, P4559 ; LIPPARI G, 1982, NATURE, V300, P197
                   ; LONDON RE, 1981, MAGNETIC RESONANCE B, V1, P1 ;
                   MCCAIN DC, 1986, J AM CHEM SOC, V108, P4259 ; NIRMALA
                   NR, 1989, J MAGN RESON, V82, P659 ; POWELL MJD, 1965,
                   COMPUT J, V7, P303 ; WEAVER AJ, 1988, BIOPHYS J, V54,
                   P1},
  isifile-dt     = {Note},
  isifile-ga     = {DH277},
  isifile-j9     = {J Amer Chem Soc},
  isifile-ji     = {J. Am. Chem. Soc.},
  isifile-nr     = {14},
  isifile-pi     = {Washington},
  isifile-rp     = {Clore, GM, NIDDKD,Chem Phys Lab,Bldg 2,Bethesda,MD
                   20892.},
  isifile-sc     = {Chemistry, Multidisciplinary},
  isifile-tc     = {463},
  issn           = {0002-7863},
  language       = {English},
  month          = {JUN 6},
  publisher      = {Amer Chemical Soc},
  size           = {3 p.},
  sourceid       = {ISI:A1990DH27700070},
  year           = 1990,
  doi            = {10.1021/ja00168a070}
}

@Article{Cordier98,
  Author         = {Cordier, F. and Caffrey, M. and Brutscher, B. and
                   Cusanovich, M. A. and Marion, D. and Blackledge, M.},
  Title          = {Solution structure, rotational diffusion anisotropy
                   and local backbone dynamics of {\em{R}hodobacter
                   capsulatus} cytochrome c2.},
  Journal        = jmb,
  Volume         = {281},
  Number         = {2},
  Pages          = {341-361},
  abstract       = {The solution structure, backbone dynamics and
                   rotational diffusion of the Rhodobacter capsulatus
                   cytochrome c2 have been determined using heteronuclear
                   NMR spectroscopy. In all, 1204 NOE-derived distances
                   were used in the structure calculation to give a final
                   ensemble with 0.59(+/-0.08) A rms deviation for the
                   backbone atoms (C, Calpha and N) with respect to the
                   mean coordinates. There is no major difference between
                   the solution structure and the previously solved X-ray
                   crystal structure (1.07(+/-0.07) A rms difference for
                   the backbone atoms), although certain significant local
                   structural differences have been identified. This
                   protein contains five helical regions and a
                   histidine-heme binding domain, connected by a series of
                   structured loops. The orientation of the helices
                   provides an excellent sampling of angular space and
                   thus allows a precise characterization of the
                   anisotropic diffusion tensor. Analysis of the
                   hydrodynamics of the protein has been performed by
                   interpretation of the 15N relaxation data using
                   isotropic, axially asymmetric and fully anisotropic
                   diffusion tensors. The protein can be shown to exhibit
                   significant anisotropic reorientation with a diffusion
                   tensor with principal axes values of
                   1.405(+/-0.031)x10(7) s-1, 1.566(+/-0.051)x10(7) s-1
                   and 1.829(+/-0.054)x10(7) s-1. Hydrodynamic
                   calculations performed on the solution structure
                   predict values of 1.399x10(7) s-1, 1.500x10(7) s-1 and
                   1.863x10(7) s-1 when a solvent shell of 3.5 A is
                   included in the calculation. The optimal orientation of
                   the diffusion tensor has been incorporated into a
                   hybrid Lipari-Szabo type local motion-anisotropic
                   rotational diffusion model to characterize the local
                   mobility in the molecule. The mobility parameters thus
                   extracted show a quantitative improvement with respect
                   to the model-free analysis assuming isotropic
                   reorientation; helical regions exhibit similar dynamic
                   properties and fewer residues require more complex
                   models of internal motion. While the molecule is
                   essentially rigid, a tripeptide loop region (residues
                   101 to 103) exhibits flexibility in the range of 20 to
                   30 ps, which appears to be correlated with the order in
                   the NMR solution structure.},
  authoraddress  = {Institut de Biologie Structurale - Jean-Pierre Ebel
                   C.N.R.S.-C.E.A., 41, Avenue des Martyrs, Grenoble
                   Cedex, 38027, France.},
  keywords       = {Algorithms ; Anisotropy ; Cytochrome c
                   Group/*chemistry ; Cytochromes c2 ; Hydrogen Bonding ;
                   *Models, Molecular ; Monte Carlo Method ; Nuclear
                   Magnetic Resonance, Biomolecular/*methods ; Protein
                   Structure, Secondary ; Protein Structure, Tertiary ;
                   Research Support, Non-U.S. Gov't ; Rhodobacter
                   capsulatus/*chemistry},
  language       = {eng},
  medline-aid    = {S0022283698919507 [pii]},
  medline-ci     = {Copyright 1998 Academic Press},
  medline-da     = {19980903},
  medline-dcom   = {19980903},
  medline-edat   = {1998/08/12},
  medline-fau    = {Cordier, F ; Caffrey, M ; Brutscher, B ; Cusanovich, M
                   A ; Marion, D ; Blackledge, M},
  medline-is     = {0022-2836},
  medline-jid    = {2985088R},
  medline-lr     = {20041117},
  medline-mhda   = {1998/08/12 00:01},
  medline-own    = {NLM},
  medline-pl     = {ENGLAND},
  medline-pmid   = {9698552},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Cytochrome c Group) ; 9035-43-2 (Cytochromes c2)},
  medline-sb     = {IM},
  medline-so     = {J Mol Biol 1998 Aug 14;281(2):341-61.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=9698552},
  year           = 1998
}

@PhdThesis{dAuvergne06,
  Author         = {d'Auvergne, E. J.},
  Title          = {Protein dynamics: a study of the model-free analysis
                   of {NMR} relaxation data.},
  School         = {Biochemistry and Molecular Biology, University of
                   Melbourne. http://eprints.infodiv.unimelb.edu.au/archive/00002799/},
  url            = {http://eprints.infodiv.unimelb.edu.au/archive/00002799/},
  year           = 2006,
  doi            = {10187/2281}
}

@Article{dAuvergneGooley03,
  Author         = {d'Auvergne, E. J. and Gooley, P. R.},
  Title          = {The use of model selection in the model-free analysis
                   of protein dynamics.},
  Journal        = jbnmr,
  Volume         = {25},
  Number         = {1},
  Pages          = {25-39},
  abstract       = {Model-free analysis of NMR relaxation data, which is
                   widely used for the study of protein dynamics, consists
                   of the separation of the global rotational diffusion
                   from internal motions relative to the diffusion frame
                   and the description of these internal motions by
                   amplitude and timescale. Five model-free models exist,
                   each of which describes a different type of motion.
                   Model-free analysis requires the selection of the model
                   which best describes the dynamics of the NH bond. It
                   will be demonstrated that the model selection technique
                   currently used has two significant flaws,
                   under-fitting, and not selecting a model when one ought
                   to be selected. Under-fitting breaks the principle of
                   parsimony causing bias in the final model-free results,
                   visible as an overestimation of S2 and an
                   underestimation of taue and Rex. As a consequence the
                   protein falsely appears to be more rigid than it
                   actually is. Model selection has been extensively
                   developed in other fields. The techniques known as
                   Akaike's Information Criteria (AIC), small sample size
                   corrected AIC (AICc), Bayesian Information Criteria
                   (BIC), bootstrap methods, and cross-validation will be
                   compared to the currently used technique. To analyse
                   the variety of techniques, synthetic noisy data
                   covering all model-free motions was created. The data
                   consists of two types of three-dimensional grid, the
                   Rex grids covering single motions with chemical
                   exchange [S2,taue,Rex], and the Double Motion grids
                   covering two internal motions [S f 2,S s 2,tau s ]. The
                   conclusion of the comparison is that for accurate
                   model-free results, AIC model selection is essential.
                   As the method neither under, nor over-fits, AIC is the
                   best tool for applying Occam's razor and has the
                   additional benefits of simplifying and speeding up
                   model-free analysis.},
  authoraddress  = {Department of Biochemistry and Molecular Biology,
                   University of Melbourne, Melbourne, Victoria 3010,
                   Australia. ejdauv@pgrad.unimelb.edu.au},
  keywords       = {Amines ; Diffusion ; *Models, Molecular ; Motion ;
                   Nuclear Magnetic Resonance, Biomolecular/*methods ;
                   Proteins/*chemistry ; Research Support, Non-U.S. Gov't
                   ; Rotation},
  language       = {eng},
  medline-aid    = {5112089 [pii]},
  medline-da     = {20030204},
  medline-dcom   = {20030926},
  medline-edat   = {2003/02/05 04:00},
  medline-fau    = {d'Auvergne, Edward J ; Gooley, Paul R},
  medline-is     = {0925-2738},
  medline-jid    = {9110829},
  medline-lr     = {20041117},
  medline-mhda   = {2003/09/27 05:00},
  medline-own    = {NLM},
  medline-pl     = {Netherlands},
  medline-pmid   = {12566997},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Amines) ; 0 (Proteins)},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR 2003 Jan;25(1):25-39.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=12566997},
  year           = 2003,
  doi            = {10.1023/a:1021902006114}
}

@Article{dAuvergneGooley06,
  Author         = {d'Auvergne, E. J. and Gooley, P. R.},
  Title          = {Model-free model elimination: {A} new step in the
                   model-free dynamic analysis of {NMR} relaxation data.},
  Journal        = jbnmr,
  Volume         = {35},
  Number         = {2},
  Pages          = {117-135},
  abstract       = {Model-free analysis is a technique commonly used
                   within the field of NMR spectroscopy to extract atomic
                   resolution, interpretable dynamic information on
                   multiple timescales from the R (1), R (2), and steady
                   state NOE. Model-free approaches employ two disparate
                   areas of data analysis, the discipline of mathematical
                   optimisation, specifically the minimisation of a chi(2)
                   function, and the statistical field of model selection.
                   By searching through a large number of model-free
                   minimisations, which were setup using synthetic
                   relaxation data whereby the true underlying dynamics is
                   known, certain model-free models have been identified
                   to, at times, fail. This has been characterised as
                   either the internal correlation times, tau( e ), tau( f
                   ), or tau( s ), or the global correlation time
                   parameter, local tau( m ), heading towards infinity,
                   the result being that the final parameter values are
                   far from the true values. In a number of cases the
                   minimised chi(2) value of the failed model is
                   significantly lower than that of all other models and,
                   hence, will be the model which is chosen by model
                   selection techniques. If these models are not removed
                   prior to model selection the final model-free results
                   could be far from the truth. By implementing a series
                   of empirical rules involving inequalities these models
                   can be specifically isolated and removed. Model-free
                   analysis should therefore consist of three distinct
                   steps: model-free minimisation, model-free model
                   elimination, and finally model-free model selection.
                   Failure has also been identified to affect the
                   individual Monte Carlo simulations used within error
                   analysis. Each simulation involves an independent
                   randomised relaxation data set and model-free
                   minimisation, thus simulations suffer from exactly the
                   same types of failure as model-free models. Therefore,
                   to prevent these outliers from causing a significant
                   overestimation of the errors the failed Monte Carlo
                   simulations need to be culled prior to calculating the
                   parameter standard deviations.},
  authoraddress  = {Department of Biochemistry and Molecular Biology,
                   Bio21 Institute of Biotechnology and Molecular Science,
                   University of Melbourne, Parkville, Victoria, 3010,
                   Australia, edward@nmr-relax.com.},
  language       = {eng},
  doi            = {10.1007/s10858-006-9007-z},
  medline-aid    = {10.1007/s10858-006-9007-z [doi]},
  medline-da     = {20060704},
  medline-dep    = {20060622},
  medline-edat   = {2006/06/23 09:00},
  medline-fau    = {d'Auvergne, Edward J ; Gooley, Paul R},
  medline-is     = {0925-2738 (Print)},
  medline-jid    = {9110829},
  medline-jt     = {Journal of biomolecular NMR.},
  medline-mhda   = {2006/06/23 09:00},
  medline-own    = {NLM},
  medline-phst   = {2005/09/15 [received] ; 2006/03/21 [accepted] ;
                   2006/06/22 [aheadofprint]},
  medline-pl     = {Netherlands},
  medline-pmid   = {16791734},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print-Electronic},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR. 2006 Jun;35(2):117-35. Epub 2006 Jun 22.},
  medline-stat   = {In-Data-Review},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=16791734},
  year           = 2006
}

@Article{dAuvergneGooley07,
  Author         = {d'Auvergne, E. J. and Gooley, P. R.},
  Title          = {Set theory formulation of the model-free problem and
                   the diffusion seeded model-free paradigm.},
  Journal        = mb,
  Volume         = {3},
  Number         = {7},
  Pages          = {483-494},
  abstract       = {Model-free analysis of NMR relaxation data, which
                   describes the motion of individual atoms, is a problem
                   intricately linked to the Brownian rotational diffusion
                   of the macromolecule. The diffusion tensor parameters
                   strongly influence the optimisation of the various
                   model-free models and the subsequent model selection
                   between them. Finding the optimal model of the dynamics
                   of the system among the numerous diffusion and
                   model-free models is hence quite complex. Using set
                   theory, the entirety of this global problem has been
                   encapsulated by the universal set Ll, and its
                   resolution mathematically formulated as the universal
                   solution Ll. Ever since the original Lipari and Szabo
                   papers the model-free dynamics of a molecule has most
                   often been solved by initially estimating the diffusion
                   tensor. The model-free models which depend on the
                   diffusion parameter values are then optimised and the
                   best model is chosen to represent the dynamics of the
                   residue. Finally, the global model of all diffusion and
                   model-free parameters is optimised. These steps are
                   repeated until convergence. For simplicity this
                   approach to Ll will be labelled the diffusion seeded
                   model-free paradigm. Although this technique suffers
                   from a number of problems many have been solved. All
                   aspects of the diffusion seeded paradigm and its
                   consequences, together with a few alternatives to the
                   paradigm, will be reviewed through the use of set
                   notation.},
  authoraddress  = {Department of Biochemistry and Molecular Biology,
                   Bio21 Institute of Biotechnology and Molecular Science,
                   University of Melbourne, Parkville, Melbourne, Victoria
                   3010, Australia.},
  keywords       = {Magnetic Resonance Spectroscopy/*methods ; *Models,
                   Theoretical ; Proteins/chemistry ; Thermodynamics},
  language       = {eng},
  doi            = {10.1039/b702202f},
  medline-aid    = {10.1039/b702202f [doi]},
  medline-da     = {20070620},
  medline-dcom   = {20070823},
  medline-dep    = {20070517},
  medline-edat   = {2007/06/21 09:00},
  medline-fau    = {d'Auvergne, Edward J ; Gooley, Paul R},
  medline-is     = {1742-206X (Print)},
  medline-jid    = {101251620},
  medline-jt     = {Molecular bioSystems},
  medline-mhda   = {2007/08/24 09:00},
  medline-own    = {NLM},
  medline-phst   = {2007/05/17 [aheadofprint] ; 2007/06/20 [epublish]},
  medline-pl     = {England},
  medline-pmid   = {17579774},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print-Electronic},
  medline-rn     = {0 (Proteins)},
  medline-sb     = {IM},
  medline-so     = {Mol Biosyst. 2007 Jul;3(7):483-94. Epub 2007 May 17.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=17579774},
  year           = 2007
}

@Article{dAuvergneGooley08a,
  Author         = {d'Auvergne, E. J. and Gooley, P. R.},
  Title          = {Optimisation of {NMR} dynamic models {I}.
                   {M}inimisation algorithms and their performance within
                   the model-free and {B}rownian rotational diffusion
                   spaces.},
  Journal        = jbnmr,
  Volume         = {40},
  Number         = {2},
  Pages          = {107-119},
  abstract       = {The key to obtaining the model-free description of the
                   dynamics of a macromolecule is the optimisation of the
                   model-free and Brownian rotational diffusion parameters
                   using the collected R (1), R (2) and steady-state NOE
                   relaxation data. The problem of optimising the
                   chi-squared value is often assumed to be trivial,
                   however, the long chain of dependencies required for
                   its calculation complicates the model-free chi-squared
                   space. Convolutions are induced by the Lorentzian form
                   of the spectral density functions, the linear
                   recombinations of certain spectral density values to
                   obtain the relaxation rates, the calculation of the NOE
                   using the ratio of two of these rates, and finally the
                   quadratic form of the chi-squared equation itself. Two
                   major topological features of the model-free space
                   complicate optimisation. The first is a long, shallow
                   valley which commences at infinite correlation times
                   and gradually approaches the minimum. The most severe
                   convolution occurs for motions on two timescales in
                   which the minimum is often located at the end of a
                   long, deep, curved tunnel or multidimensional valley
                   through the space. A large number of optimisation
                   algorithms will be investigated and their performance
                   compared to determine which techniques are suitable for
                   use in model-free analysis. Local optimisation
                   algorithms will be shown to be sufficient for
                   minimisation not only within the model-free space but
                   also for the minimisation of the Brownian rotational
                   diffusion tensor. In addition the performance of the
                   programs Modelfree and Dasha are investigated. A number
                   of model-free optimisation failures were identified:
                   the inability to slide along the limits, the singular
                   matrix failure of the Levenberg-Marquardt minimisation
                   algorithm, the low precision of both programs, and a
                   bug in Modelfree. Significantly, the singular matrix
                   failure of the Levenberg-Marquardt algorithm occurs
                   when internal correlation times are undefined and is
                   greatly amplified in model-free analysis by both the
                   grid search and constraint algorithms. The program
                   relax ( http://www.nmr-relax.com ) is also presented as
                   a new software package designed for the analysis of
                   macromolecular dynamics through the use of NMR
                   relaxation data and which alleviates all of the
                   problems inherent within model-free analysis.},
  authoraddress  = {Department of NMR-based Structural Biology, Max Planck
                   Institute for Biophysical Chemistry, Am Fassberg 11,
                   D-37077, Goettingen, Germany. edward@nmr-relax.com},
  keywords       = {*Algorithms ; Cytochromes c2/chemistry ; Diffusion ;
                   *Models, Molecular ; Nuclear Magnetic Resonance,
                   Biomolecular/*methods ; Rhodobacter
                   capsulatus/chemistry ; *Rotation},
  language       = {eng},
  doi            = {10.1007/s10858-007-9214-2},
  medline-aid    = {10.1007/s10858-007-9214-2 [doi]},
  medline-crdt   = {2007/12/19 09:00},
  medline-da     = {20080109},
  medline-dcom   = {20080917},
  medline-dep    = {20071218},
  medline-edat   = {2007/12/19 09:00},
  medline-fau    = {d'Auvergne, Edward J ; Gooley, Paul R},
  medline-is     = {0925-2738 (Print) ; 0925-2738 (Linking)},
  medline-jid    = {9110829},
  medline-jt     = {Journal of biomolecular NMR},
  medline-lr     = {20091118},
  medline-mhda   = {2008/09/18 09:00},
  medline-oid    = {NLM: PMC2758376},
  medline-own    = {NLM},
  medline-phst   = {2007/02/23 [received] ; 2007/11/06 [accepted] ;
                   2007/12/18 [aheadofprint]},
  medline-pl     = {Netherlands},
  medline-pmc    = {PMC2758376},
  medline-pmid   = {18085410},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-rn     = {9035-43-2 (Cytochromes c2)},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR. 2008 Feb;40(2):107-19. Epub 2007 Dec 18.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=18085410},
  year           = 2008
}

@Article{dAuvergneGooley08b,
  Author         = {d'Auvergne, E. J. and Gooley, P. R.},
  Title          = {Optimisation of {NMR} dynamic models {II}. {A} new
                   methodology for the dual optimisation of the model-free
                   parameters and the {B}rownian rotational diffusion
                   tensor.},
  Journal        = jbnmr,
  Volume         = {40},
  Number         = {2},
  Pages          = {121-133},
  abstract       = {Finding the dynamics of an entire macromolecule is a
                   complex problem as the model-free parameter values are
                   intricately linked to the Brownian rotational diffusion
                   of the molecule, mathematically through the
                   autocorrelation function of the motion and
                   statistically through model selection. The solution to
                   this problem was formulated using set theory as an
                   element of the universal set [formula: see text]-the
                   union of all model-free spaces (d'Auvergne EJ and
                   Gooley PR (2007) Mol BioSyst 3(7), 483-494). The
                   current procedure commonly used to find the universal
                   solution is to initially estimate the diffusion tensor
                   parameters, to optimise the model-free parameters of
                   numerous models, and then to choose the best model via
                   model selection. The global model is then optimised and
                   the procedure repeated until convergence. In this paper
                   a new methodology is presented which takes a different
                   approach to this diffusion seeded model-free paradigm.
                   Rather than starting with the diffusion tensor this
                   iterative protocol begins by optimising the model-free
                   parameters in the absence of any global model
                   parameters, selecting between all the model-free
                   models, and finally optimising the diffusion tensor.
                   The new model-free optimisation protocol will be
                   validated using synthetic data from Schurr JM et al.
                   (1994) J Magn Reson B 105(3), 211-224 and the
                   relaxation data of the bacteriorhodopsin (1-36)BR
                   fragment from Orekhov VY (1999) J Biomol NMR 14(4),
                   345-356. To demonstrate the importance of this new
                   procedure the NMR relaxation data of the Olfactory
                   Marker Protein (OMP) of Gitti R et al. (2005) Biochem
                   44(28), 9673-9679 is reanalysed. The result is that the
                   dynamics for certain secondary structural elements is
                   very different from those originally reported.},
  authoraddress  = {Department of NMR-based Structural Biology, Max Planck
                   Institute for Biophysical Chemistry, Am Fassberg 11,
                   Goettingen, D-37077, Germany. edward@nmr-relax.com},
  keywords       = {Algorithms ; Amides/chemistry ;
                   Bacteriorhodopsins/chemistry ; Crystallography, X-Ray ;
                   Diffusion ; *Models, Molecular ; Nuclear Magnetic
                   Resonance, Biomolecular/*methods ; Olfactory Marker
                   Protein/chemistry ; Peptide Fragments/chemistry ;
                   Protein Structure, Secondary ; *Rotation},
  language       = {eng},
  doi            = {10.1007/s10858-007-9213-3},
  medline-aid    = {10.1007/s10858-007-9213-3 [doi]},
  medline-crdt   = {2007/12/19 09:00},
  medline-da     = {20080109},
  medline-dcom   = {20080917},
  medline-dep    = {20071218},
  medline-edat   = {2007/12/19 09:00},
  medline-fau    = {d'Auvergne, Edward J ; Gooley, Paul R},
  medline-is     = {0925-2738 (Print) ; 0925-2738 (Linking)},
  medline-jid    = {9110829},
  medline-jt     = {Journal of biomolecular NMR},
  medline-lr     = {20091118},
  medline-mhda   = {2008/09/18 09:00},
  medline-oid    = {NLM: PMC2758375},
  medline-own    = {NLM},
  medline-phst   = {2007/02/23 [received] ; 2007/11/06 [accepted] ;
                   2007/12/18 [aheadofprint]},
  medline-pl     = {Netherlands},
  medline-pmc    = {PMC2758375},
  medline-pmid   = {18085411},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-rn     = {0 (Amides) ; 0 (Olfactory Marker Protein) ; 0 (Peptide
                   Fragments) ; 53026-44-1 (Bacteriorhodopsins)},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR. 2008 Feb;40(2):121-33. Epub 2007 Dec 18.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=18085411},
  year           = 2008
}

@Article{dAuvergneGooley08ab,
  Author         = {d'Auvergne, E. J. and Gooley, P. R.},
  Title          = {Optimisation of {NMR} dynamic models},
  Journal        = jbnmr,
  Volume         = {40},
  Number         = {2},
  Pages          = {107-133},
  year           = 2008
}

@Article{Davis94,
  Author         = {Davis, D.G. and Perlman, M.E. and London, R.E.},
  Title          = {Direct measurements of the dissociation-rate constant
                   for inhibitor-enzyme complexes via the {T}1rho and {T}2
                   ({CPMG}) methods},
  Journal        = jmr,
  Volume         = {104},
  Number         = {3},
  Pages          = {266-275},
  abstract       = {The unimolecular dissociation rate constant, k(-1),
                   for the inhibitor-enzyme complex tubercidin-Escherichia
                   coli purine nucleoside phosphorylase (PNPase) has been
                   determined directly via two related H-1 NMR methods for
                   studying exchange-mediated transverse relaxation. One
                   method involves measurements of the decay rate, 1/T-1
                   rho, of spin-locked magnetization in the rotating frame
                   as a function of the strength of the spin-locking
                   field, omega(SL) The second method involves
                   measurements of the Carr-Purcell-Meiboom-Gill (CPMG)
                   spin-echo decay rate, 1/T-2(CPMG) as a function of the
                   repetition rate, 1/t(cp), of the refocusing pulses.
                   Expressions describing the dependence of T-2(CPMG) as a
                   function of 1/t(cp) and k(-1) have been previously
                   derived with sufficient generality to include the
                   two-site inhibitor-enzyme exchange case. Existing
                   expressions for T-1 rho as a function of k(ex) and
                   omega(SL), however, had to be reformulated to take into
                   account differences between T-2(b) and T-1(b) for the
                   bound form of the inhibitor as well as offset
                   corrections important at low values of omega(SL) A new
                   expression for exchange-mediated T-1 rho has been
                   derived to take these factors into account and is shown
                   to provide a more accurate description of observed T-1
                   rho data than previous models. Numerical analysis of
                   relaxation rates, measured independently by either the
                   rotating-frame or the spin-echo method for the H-1 and
                   H-2 protons of tubercidin at different inhibitor:enzyme
                   ratios, yields comparable values for k(-1) of 2400
                   (+/-350) and 900 (+/-80) s(-1) at 20 and 10 degrees C,
                   respectively. The merits of both methods are compared
                   and suggestions for optimizing the experiments are
                   discussed. (C) 1994 Academic Press, Inc.},
  address        = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495},
  affiliation    = {DAVIS, DG (Reprint Author), NIEHS,MOLEC BIOPHYS
                   LAB,POB 12233,RES TRIANGLE PK,NC 27709, USA.},
  doc-delivery-number = {NX809},
  doi            = {10.1006/jmrb.1994.1084},
  issn           = {1064-1866},
  journal-iso    = {J. Magn. Reson. Ser. B},
  keywords-plus  = {RELAXATION-MATRIX ANALYSIS; SPIN-LATTICE RELAXATION;
                   CHEMICAL EXCHANGE; ROTATING FRAME; NUCLEAR;
                   CONFORMATIONS; PROTEINS; T2},
  language       = {English},
  month          = {JUL},
  number-of-cited-references = {34},
  publisher      = {ACADEMIC PRESS INC JNL-COMP SUBSCRIPTIONS},
  research-areas = {Physics},
  times-cited    = {182},
  type           = {Article},
  unique-id      = {ISI:A1994NX80900008},
  web-of-science-categories = {Physics, Atomic, Molecular \& Chemical},
  year           = 1994
}

@Article{DellwoWand89,
  Author         = {Dellwo, M. J. and Wand, A. J.},
  Title          = {Model-independent and model-dependent analysis of the
                   global and internal dynamics of cyclosporine-{A}},
  Journal        = jacs,
  Volume         = {111},
  Number         = {13},
  Pages          = {4571-4578},
  address        = {1155 16th ST, NW, Washington, DC 20036},
  authoraddress  = {Fox Chase Canc Ctr,Inst Canc Res,7701 Burholme
                   Ave,Philadelphia,PA 19111.},
  citedref       = {ABRAGAM A, 1961, PRINCIPLES NUCLEAR M, P313 ; CANTOR
                   CR, 1980, BIOPHYSIAL CHEM 2, P500 ; CRESPI HL, 1982,
                   METHOD ENZYMOL, V88, P3 ; CRIPPEN GM, 1981, DISTANCE
                   GEOMETRY CO ; DEBRUNNER PG, 1982, ANNU REV PHYS CHEM,
                   V33, P283 ; DUFOURC EJ, 1983, CHEM PHYS LIPIDS, V33,
                   P153 ; ENGLANDER SW, 1984, Q REV BIOPHYS, V16, P521 ;
                   ERNST RR, 1987, PRINCIPLES NUCLEAR M ; JANIN J, 1983,
                   PROG BIOPHYS MOL BIO, V42, P21 ; JARRELL HC, 1987,
                   BIOCHIM BIOPHYS ACTA, V897, P69 ; KARPLUS M, 1981, CRC
                   CRIT REV BIOCH, V9, P293 ; KESSLER H, 1985, HELV CHIM
                   ACTA, V68, P661 ; KESSLER H, 1988, ANGEW CHEM INT EDIT,
                   V27, P450 ; LAUTZ J, 1987, J COMPUTER AIDED MOL, V1,
                   P219 ; LEMASTER DM, 1982, ANAL BIOCHEM, V122, P238 ;
                   LEMASTER DM, 1982, J BIOL CHEM, V257, P1224 ; LEMASTER
                   DM, 1988, FEBS LETT, V236, P71 ; LIPARI G, 1980,
                   BIOPHYS J, V30, P489 ; LIPARI G, 1982, J AM CHEM SOC,
                   V104, P4546 ; LIPARI G, 1982, J AM CHEM SOC, V104,
                   P4559 ; LIPARI G, 1982, NATURE, V300, P197 ; LONDON RE,
                   1978, J AM CHEM SOC, V100, P7159 ; LOOSLI HR, 1985,
                   HELV CHIM ACTA, V68, P682 ; MARTIN ML, 1980, PRACTICAL
                   NMR SPECTR, P244 ; MCCAIN DC, 1986, J AM CHEM SOC,
                   V108, P4259 ; MCCAIN DC, 1987, J MAGN RESON, V73, P244
                   ; MCCAMMON JA, 1977, NATURE, V267, P585 ; NORTON RS,
                   1977, J AM CHEM SOC, V99, P79 ; WALLACH D, 1967, J CHEM
                   PHYS, V47, P5258 ; WEAST RC, 1982, CRC HDB CHEM
                   PHYSICS, F41 ; WEAVER AJ, 1988, BIOPHYS J, V54, P1 ;
                   WEHRLI FW, 1980, INTERPRETATION CARBO, P133 ; WITTEBORT
                   RJ, 1978, J CHEM PHYS, V69, P1722 ; WOESSNER DE, 1962,
                   J CHEM PHYS, V36, P1},
  isifile-dt     = {Article},
  isifile-ga     = {AC962},
  isifile-j9     = {J Amer Chem Soc},
  isifile-ji     = {J. Am. Chem. Soc.},
  isifile-nr     = {34},
  isifile-pi     = {Washington},
  isifile-sc     = {Chemistry, Multidisciplinary},
  isifile-tc     = {98},
  issn           = {0002-7863},
  language       = {English},
  month          = {Jun 21},
  publisher      = {Amer Chemical Soc},
  size           = {8 p.},
  sourceid       = {ISI:A1989AC96200007},
  year           = 1989
}

@Article{Dosset00,
  Author         = {Dosset, P. and Hus, J. C. and Blackledge, M. and
                   Marion, D.},
  Title          = {Efficient analysis of macromolecular rotational
                   diffusion from heteronuclear relaxation data.},
  Journal        = jbnmr,
  Volume         = {16},
  Number         = {1},
  Pages          = {23-28},
  abstract       = {A novel program has been developed for the
                   interpretation of 15N relaxation rates in terms of
                   macromolecular anisotropic rotational diffusion. The
                   program is based on a highly efficient simulated
                   annealing/minimization algorithm, designed specifically
                   to search the parametric space described by the
                   isotropic, axially symmetric and fully anisotropic
                   rotational diffusion tensor models. The high efficiency
                   of this algorithm allows extensive noise-based Monte
                   Carlo error analysis. Relevant statistical tests are
                   systematically applied to provide confidence limits for
                   the proposed tensorial models. The program is
                   illustrated here using the example of the cytochrome c'
                   from Rhodobacter capsulatus, a four-helix bundle heme
                   protein, for which data at three different field
                   strengths were independently analysed and compared.},
  authoraddress  = {Institut de Biologie Structurale--Jean-Pierre Ebel,
                   C.N.R.S.-C.E.A., Grenoble, France.},
  keywords       = {*Algorithms ; Diffusion ; *Models, Chemical ;
                   Nitrogen/*chemistry ; Nitrogen Isotopes ; Nuclear
                   Magnetic Resonance, Biomolecular/*methods ; Research
                   Support, Non-U.S. Gov't ; *Software},
  language       = {eng},
  medline-da     = {20000404},
  medline-dcom   = {20000404},
  medline-edat   = {2000/03/16},
  medline-fau    = {Dosset, P ; Hus, J C ; Blackledge, M ; Marion, D},
  medline-is     = {0925-2738},
  medline-jid    = {9110829},
  medline-lr     = {20041117},
  medline-mhda   = {2000/03/16 00:01},
  medline-own    = {NLM},
  medline-pl     = {NETHERLANDS},
  medline-pmid   = {10718609},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Nitrogen Isotopes) ; 7727-37-9 (Nitrogen)},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR 2000 Jan;16(1):23-8.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=10718609},
  year           = 2000
}

@Book{Edwards72,
  Author         = {A. W. F. Edwards},
  Title          = {Likelihood},
  Publisher      = {Cambridge University Press},
  Address        = {London},
  description    = {"The book is indeed a classic. Virtually every
                   philosopher of science now writing about probabilistic
                   inference has been influenced by Edwards' book, and his
                   ideas are now as alive and relevant as they were when
                   the book first appeared. Edwards is an absolutely
                   seminal thinker in the foundations of statistics and
                   scientific inference."--Elliott Sober, University of
                   Wisconsin-Madison. "Full of appropriate examples
                   (especially from genetics) and historical commentary,
                   this monograph offers a rare simultaneous treatment of
                   both mathematical and philosophical foundations."--
                   American Mathematical Monthly. This new and expanded
                   edition of A. W. F. Edwards' classic volume on
                   scientific inference presents his most important
                   published articles on the subject. Edwards argues that
                   the appropriate axiomatic basis for inductive inference
                   is not that of probability, with its addition axiom,
                   but that of likelihood, the concept introduced by
                   Fisher as a measure of relative support among different
                   hypotheses. Starting from the simplest considerations
                   and assuming no more than a basic acquaintancewith
                   probability theory, the author sets out to reconstruct
                   a consistent theory of statistical inference in
                   science. Using the likelihood approach, he explores
                   estimation, tests of significance, randomization,
                   experimental design, and other statistical topics.
                   Likelihood is important reading for students and
                   professionals in biology, mathematical sciences, and
                   philosophy. "This book is commended to all philosophers
                   of science who are interested in the problems of
                   scientific inference."-- Search. "This book, by a
                   well-known geneticist, will do much to publicize the
                   generality of the likelihood method as a foundation for
                   statistical procedure. It is both smoothly written and
                   persuasive."-- Operations Research. " Likelihood is an
                   important text and, in addition, is a joy to read,
                   being a paragon of lucid and witty exposition."--
                   Mathematical Gazette},
  year           = 1972
}

@Article{Einstein05,
  Author         = {Einstein, A.},
  Title          = {{\"U}ber die von der molekularkinetischen {T}heorie der
                   {W}\"arme geforderte {B}ewegung von in ruhenden
                   {F}l\"ussigkeiten suspendierten {T}eilchen ({T}he motion of
                   elements suspended in static liquids as claimed in the
                   molecular kinetic theory of heat)},
  Journal        = ap,
  Volume         = {17},
  Number         = {8},
  Pages          = {549-560},
  address        = {PO Box 10 11 61, D-69451 Weinheim, Germany},
  citedref       = {1902, ANN PHYS, V9, P417 ; 1903, ANN PHYS, V11, P170 ;
                   EINSTEIN A, 1903, ANN PHYS-BERLIN, V11, P170 ;
                   KIRCHHOFF BG, VOILESUNGEN MECH},
  isifile-dt     = {Article},
  isifile-ga     = {V29LZ},
  isifile-j9     = {Ann Phys-Berlin},
  isifile-ji     = {Ann. Phys.-Berlin},
  isifile-nr     = {4},
  isifile-pi     = {Weinheim},
  isifile-sc     = {Physics, Multidisciplinary},
  isifile-tc     = {1566},
  issn           = {0003-3804},
  language       = {German},
  month          = {Jul},
  publisher      = {Wiley-V C H Verlag GMBH},
  size           = {12 p.},
  sourceid       = {ISI:000201991500005},
  year           = 1905,
  doi            = {10.1002/andp.19053220806}
}


@Article{Erdelyi11,
  Author = {Erdelyi, Mate and d'Auvergne, Edward and Navarro-Vazquez, Armando and
     Leonov, Andrei and Griesinger, Christian},
  Title = {Dynamics of the Glycosidic Bond: Conformational Space of Lactose},
  Journal = cej,
  Year = {2011},
  Volume = {17},
  Number = {34},
  Pages = {9368-9376},
  Month = {AUG 16},
  Abstract = {The dynamics of the glycosidic bond of lactose was studied by a
     paramagnetic tagging-based NMR technique, which allowed the collection
     of an unusually large series of NMR data for a single compound. By the
     use of distance-and orientation-dependent residual dipolar couplings and
     pseudocontact shifts, the simultaneous fitting of the probabilities of
     computed conformations and the orientation of the magnetic
     susceptibility tensor of a series of lanthanide complexes of lactose
     show that its glycosidic bond samples syn/syn, anti/syn and syn/anti
     phi/psi regions of the conformational space in water. The analysis
     indicates a higher reliability of pseudocontact shift data as compared
     to residual dipolar couplings with the presently available weakly
     orienting paramagnetic tagging technique. The method presented herein
     allows for an improved understanding of the dynamic behaviour of
     oligosaccharides.},
  Publisher = {WILEY-BLACKWELL},
  Address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA},
  Type = {Article},
  Language = {English},
  Affiliation = {Griesinger, C (Reprint Author), Max Planck Inst Biophys Chem, NMR Based Struct Biol, Fassberg 11, D-37077 Gottingen, Germany.
     Erdelyi, Mate; d'Auvergne, Edward; Leonov, Andrei; Griesinger, Christian, Max Planck Inst Biophys Chem, NMR Based Struct Biol, D-37077 Gottingen, Germany.
     Erdelyi, Mate, Gothenburg Univ, Dept Chem, S-41124 Gothenburg, Sweden.
     Erdelyi, Mate, Gothenburg Univ, Swedish NMR Ctr, S-41124 Gothenburg, Sweden.
     Navarro-Vazquez, Armando, Univ Vigo, Dept Organ Chem, Vigo, Spain.},
  DOI = {10.1002/chem.201100854},
  ISSN = {0947-6539},
  Keywords = {glycosidic bonds; molecular dynamics; NMR spectroscopy;
     oligosaccharides; paramagnetism},
  Keywords-Plus = {RICIN-B-CHAIN; RESIDUAL DIPOLAR COUPLINGS; MODEL-FREE; CONVENIENT
     SYNTHESIS; MOLECULAR MECHANICS; WEAK ALIGNMENT; FORCE-FIELD; NMR;
     FLEXIBILITY; PROTEINS},
  Subject-Category = {Chemistry},
  Web-of-Science-Category = {Chemistry, Multidisciplinary},
  Author-Email = {cigr@nmr.mpibpc.mpg.de},
  Funding-Acknowledgement = {Max Planck Society; Swedish Research Council\{{[}\}2004-3073, 2007-4407];
     Spanish Ministerio de Ciencia e Innovacin; Xunta de Galicia (Conselleria
     de Educacion)\{{[}\}2009/071]},
  Funding-Text = {This work was supported by the Max Planck Society (to C.G.) and the
     Swedish Research Council (2004-3073, 2007-4407 to M.E.). A.N.V thanks
     Spanish Ministerio de Ciencia e Innovacin for a ``Ramon y Cajal\{''\}
     research contract and Xunta de Galicia/FEDER (Conselleria de Educacion
     2009/071) for financial support.},
  Number-of-Cited-References = {62},
  Times-Cited = {0},
  Journal-ISO = {Chem.-Eur. J.},
  Doc-Delivery-Number = {818VR},
  Unique-ID = {ISI:000294784400016},
}

@Article{Farrow94,
  Author         = {Farrow, N. A. and Muhandiram, R. and Singer, A. U. and
                   Pascal, S. M. and Kay, C. M. and Gish, G. and Shoelson,
                   S. E. and Pawson, T. and Forman-Kay, J. D. and Kay, L.
                   E.},
  Title          = {Backbone dynamics of a free and
                   phosphopeptide-complexed {S}rc homology 2 domain
                   studied by 15{N} {NMR} relaxation.},
  Journal        = biochem,
  Volume         = {33},
  Number         = {19},
  Pages          = {5984-6003},
  abstract       = {The backbone dynamics of the C-terminal SH2 domain of
                   phospholipase C gamma 1 have been investigated. Two
                   forms of the domain were studied, one in complex with a
                   high-affinity binding peptide derived from the
                   platelet-derived growth factor receptor and the other
                   in the absence of this peptide. 2-D 1H-15N NMR methods,
                   employing pulsed field gradients, were used to
                   determine steady-state 1H-15N NOE values and T1 and T2
                   15N relaxation times. Backbone dynamics were
                   characterized by the overall correlation time (tau m),
                   order parameters (S2), effective correlation times for
                   internal motions (tau e), and, if required, terms to
                   account for motions on a
                   microsecond-to-millisecond-time scale. An extended
                   two-time-scale formalism was used for residues having
                   relaxation data and that could not be fit adequately
                   using a single-time-scale formalism. The overall
                   correlation times of the uncomplexed and complexed
                   forms of SH2 were found to be 9.2 and 6.5 ns,
                   respectively, suggesting that the uncomplexed form is
                   in a monomer-dimer equilibrium. This was subsequently
                   confirmed by hydrodynamic measurements. Analysis of
                   order parameters reveals that residues in the so-called
                   phosphotyrosine-binding loop exhibited higher than
                   average disorder in both forms of SH2. Although
                   localized differences in order parameters were observed
                   between the uncomplexed and complexed forms of SH2,
                   overall, higher order parameters were not found in the
                   peptide-bound form, indicating that on average,
                   picosecond-time-scale disorder is not reduced upon
                   binding peptide. The relaxation data of the
                   SH2-phosphopeptide complex were fit with fewer exchange
                   terms than the uncomplexed form. This may reflect the
                   monomer-dimer equilibrium that exists in the
                   uncomplexed form or may indicate that the complexed
                   form has lower conformational flexibility on a
                   microsecond-to-millisecond-time scale.},
  authoraddress  = {Protein Engineering Network Centres of Excellence,
                   University of Toronto, Ontario, Canada.},
  keywords       = {Amino Acid Sequence ; Cloning, Molecular ; Escherichia
                   coli/genetics ; Isoenzymes/chemistry ; Magnetic
                   Resonance Spectroscopy ; Models, Chemical ; Molecular
                   Sequence Data ; Nitrogen Isotopes ; Phospholipase
                   C/chemistry ; Phosphopeptides/*chemistry ; Protein
                   Binding ; Protein Structure, Secondary ; Proto-Oncogene
                   Protein pp60(c-src)/*chemistry ; Recombinant
                   Proteins/chemistry ; Research Support, Non-U.S. Gov't ;
                   Sequence Homology, Amino Acid},
  language       = {eng},
  medline-da     = {19940616},
  medline-dcom   = {19940616},
  medline-edat   = {1994/05/17},
  medline-fau    = {Farrow, N A ; Muhandiram, R ; Singer, A U ; Pascal, S
                   M ; Kay, C M ; Gish, G ; Shoelson, S E ; Pawson, T ;
                   Forman-Kay, J D ; Kay, L E},
  medline-is     = {0006-2960},
  medline-jid    = {0370623},
  medline-lr     = {20041117},
  medline-mhda   = {1994/05/17 00:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {7514039},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Isoenzymes) ; 0 (Nitrogen Isotopes) ; 0
                   (Phosphopeptides) ; 0 (Recombinant Proteins) ; EC
                   2.7.1.112 (Proto-Oncogene Protein pp60(c-src)) ; EC
                   3.1.4.- (phospholipase C gamma) ; EC 3.1.4.3
                   (Phospholipase C)},
  medline-sb     = {IM},
  medline-so     = {Biochemistry 1994 May 17;33(19):5984-6003.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=7514039},
  year           = 1994
}

@Article{Farrow95,
  Author         = {Farrow, N. A. and Zhang, O. W. and Szabo, A. and
                   Torchia, D. A. and Kay, L. E.},
  Title          = {Spectral density-function mapping using
                   {N}-15 relaxation data exclusively},
  Journal        = jbnmr,
  Volume         = {6},
  Number         = {2},
  Pages          = {153-162},
  abstract       = {A method is presented for the determination of values
                   of the spectral density function, J(omega), describing
                   the dynamics of amide bond vectors from N-15 relaxation
                   parameters alone. Assuming that the spectral density is
                   given by the sum of Lorentzian functions, the approach
                   allows values of J(omega) to be obtained at omega=0,
                   omega(N), and 0.870 omega(H), where omega(N) and
                   omega(H) are Larmor frequencies of nitrogen and proton
                   nuclei, respectively, from measurements of N-15 T-1,
                   T-2 and H-1-N-15 steady-state NOE values at a single
                   spectrometer frequency. Alternatively, when
                   measurements are performed at two different
                   spectrometer frequencies of i and j MHz, J(omega) can
                   be mapped at omega=0, omega(N)(i), omega(N)(j), 0.870
                   omega(H)(i) and 0.870 omega Hj, where omega Ni, for
                   example, is the N-15 Larmor frequency for a
                   spectrometer operating at i MHz. Additionally,
                   measurements made at two different spectrometer
                   frequencies enable contributions to transverse
                   relaxation from motions on millisecond-microsecond time
                   scales to be evaluated and permit assessment of whether
                   a description of the internal dynamics is consistent
                   with a correlation function describing the dynamics of
                   the N-15-NH bond vector are necessary, provided that
                   dJ(omega)/d omega is relatively constant between
                   omega=omega(H) + omega(N) to omega=omega(H)-omega(N).
                   Simulations demonstrate that the method is accurate for
                   a wide range of protein motions and correlation times,
                   and experimental data establish the validity of the
                   methodology. Results are presented for a folded and an
                   unfolded form of the N-terminal SH3 domain of the
                   protein drk.},
  month          = {Sep},
  sourceid       = {ISI:A1995RY39200006},
  year           = 1995,
  doi            = {10.1007/bf00211779}
}

@Article{Favro60,
  Author         = {Favro, L. D.},
  Title          = {Theory of the rotational brownian motion of a free
                   rigid body},
  Journal        = physrev,
  Volume         = {119},
  Number         = {1},
  Pages          = {53-62},
  abstract       = {The orientation of a rigid body is specified by the
                   Cayley-Klein parameters. A system of such bodies
                   subject to small random changes in orientation but not
                   subject to any externally applied torque is then
                   considered in some detail. A diffusion equation is
                   derived with certain linear combinations of the
                   Cayley-Klein parameters as independent variables. This
                   equation is expressed in terms of quantum-mechanical
                   angular momentum operators and a Green's function for
                   the equation is obtained as an expansion in angular
                   momentum eigenfunctions. This expansion can be used to
                   calculate averages of various physical quantities in a
                   nonequilibrium distribution of orientations. It may
                   also be used to calculate the spectral density of
                   fluctuating quantities in an equilibrium distribution.
                   Illustrative examples of both of these applications are
                   given.},
  address        = {One Physics Ellipse, College PK, MD 20740-3844 USA},
  citedref       = {EDWARDES D, 1892, Q J MATH, V26, P70 ; FURRY WH, 1957,
                   PHYS REV, V107, P7 ; FURTH R, 1956, INVESTIGATIONS
                   THEOR ; GOLDSTEIN H, 1950, CLASSICAL MECHANICS, P109 ;
                   HUBBARD PS, 1958, PHYS REV, V109, P1153 ; KHINTCHINE A,
                   1934, MATH ANN, V109, P604 ; PERRIN F, 1934, J
                   PHYS-PARIS, V5, P497 ; WAX N, 1954, NOISE STOCHASTIC
                   PRO ; WHITTAKER ET, 1927, MODERN ANALYSIS, P281 ;
                   WIENER N, 1930, ACTA MATH-DJURSHOLM, V55, P117},
  isifile-dt     = {Article},
  isifile-ga     = {WB798},
  isifile-j9     = {Phys Rev},
  isifile-nr     = {10},
  isifile-pi     = {College PK},
  isifile-sc     = {Physics, Multidisciplinary},
  isifile-tc     = {315},
  issn           = {0031-899X},
  language       = {English},
  publisher      = {American Physical Soc},
  size           = {10 p.},
  sourceid       = {ISI:A1960WB79800009},
  year           = 1960,
  doi            = {10.1103/PhysRev.119.53}
}

@Article{Fletcher70,
  Author         = {Fletcher, R.},
  Title          = {A new approach to variable metric algorithms},
  Journal        = cj,
  Volume         = {13},
  Number         = {3},
  Pages          = {317-322},
  abstract       = {An approach to variable metric algorithms has been
                   investigated in which the linear search sub-problem no
                   longer becomes necessary. The property of quadratic
                   termination has been replaced by one of monotonic
                   convergence of the eigenvalues of the approximating
                   matrix to the inverse hessian. A convex class of
                   updating formulae which possess this property has been
                   established, and a strategy has been indicated for
                   choosing a member of the class so as to keep the
                   approximation away from both singularity and
                   unboundedness. A FORTRAN program has been tested
                   extensively with encouraging results. },
  doi            = {10.1093/comjnl/13.3.317},
  eprint         = {http://comjnl.oxfordjournals.org/cgi/reprint/13/3/317.pdf},
  url            = {http://comjnl.oxfordjournals.org/cgi/content/abstract/13/3/317},
  year           = 1970
}

@Article{FletcherReeves64,
  Author         = {Fletcher, R. and Reeves, C. M.},
  Title          = {Function minimization by conjugate gradients},
  Journal        = cj,
  Volume         = {7},
  Number         = {2},
  Pages          = {149-154},
  abstract       = {A quadratically convergent gradient method for
                   locating an unconstrained local minimum of a function
                   of several variables is described. Particular
                   advantages are its simplicity and its modest demands on
                   storage, space for only three vectors being required.
                   An ALGOL procedure is presented, and the paper includes
                   a discussion of results obtained by its used on various
                   test functions. },
  doi            = {10.1093/comjnl/7.2.149},
  eprint         = {http://comjnl.oxfordjournals.org/cgi/reprint/7/2/149.pdf},
  url            = {http://comjnl.oxfordjournals.org/cgi/content/abstract/7/2/149},
  year           = 1964
}

@Article{Fushman97,
  Author         = {Fushman, D. and Cahill, S. and Cowburn, D.},
  Title          = {The main-chain dynamics of the dynamin pleckstrin
                   homology ({PH}) domain in solution: analysis of 15{N}
                   relaxation with monomer/dimer equilibration.},
  Journal        = jmb,
  Volume         = {266},
  Number         = {1},
  Pages          = {173-194},
  abstract       = {The backbone dynamics of the pleckstrin homology (PH)
                   domain from dynamin were studied by 15N NMR relaxation
                   (R1 and R2) and steady state heteronuclear 15N [1H]
                   nuclear Overhauser effect measurements at 500 and 600
                   MHz, at protein concentrations of 1.7 mM and 300
                   microM, and by molecular dynamics (MD) simulations. The
                   analysis was performed using the model-free approach.
                   The method was extended in order to account for
                   observed partial (equilibrium) dimerization of the
                   protein at NMR concentrations. A model is developed
                   that takes into account both rapid monomer-dimer
                   exchange and anisotropy of the over-all rotation of the
                   dimer. The data show complex dynamics of the dynamin PH
                   domain. Internal motions in elements of the secondary
                   structure are restricted, as inferred from the high
                   value of the order parameter (S2 approximately 0.9) and
                   from the local correlation time < 100 ps. Of the four
                   extended loop regions that are disordered in the
                   NMR-derived solution structure of the protein, loops
                   beta 1/beta 2 and beta 5/beta 6 are involved in a
                   large-amplitude (S2 down to 0.2 to 0.3) subnanosecond
                   to nanosecond time-scale motion. Reorientation of the
                   loops beta 3/beta 4 and beta 6/beta 7, in contrast, is
                   restricted, characterized by the values of order
                   parameter S2 approximately 0.9 more typical of the
                   protein core. These loops, however, are involved in
                   much slower processes of motion resulting in a
                   conformational exchange on a microsecond to
                   submillisecond time scale. The motions of the terminal
                   regions (residues 1 to 10, 122 to 125) are practically
                   unrestricted (S2 down to 0.05, characteristic times in
                   nanosecond time scale), suggesting that these parts of
                   the sequence do not participate in the protein fold.
                   The analysis shows a larger sensitivity of the 15N
                   relaxation data to protein microdynamic parameters (S2,
                   tau loc) when protein molecular mass (tau c) increases.
                   The use of negative values of the steady state 15N[1H]
                   NOEs as an indicator of the residues not belonging to
                   the folded structure is suggested. The amplitudes of
                   local motion observed in the MD simulation are in a
                   good-agreement with the NMR data for the amide NH
                   groups located in the protein core.},
  authoraddress  = {Rockefeller University, New York, NY 10021, USA.},
  keywords       = {Blood Proteins/*chemistry ; Comparative Study ;
                   Computer Simulation ; Dynamins ; GTP
                   Phosphohydrolases/*chemistry ; Kinetics ;
                   Macromolecular Substances ; Magnetic Resonance
                   Spectroscopy ; Nitrogen Isotopes ; *Phosphoproteins ;
                   *Protein Structure, Secondary ; Recombinant
                   Proteins/chemistry ; Research Support, Non-U.S. Gov't ;
                   Sequence Homology, Amino Acid},
  language       = {eng},
  medline-aid    = {S0022283696907718 [pii]},
  medline-da     = {19970403},
  medline-dcom   = {19970403},
  medline-edat   = {1997/02/14},
  medline-fau    = {Fushman, D ; Cahill, S ; Cowburn, D},
  medline-is     = {0022-2836},
  medline-jid    = {2985088R},
  medline-lr     = {20041117},
  medline-mhda   = {1997/02/14 00:01},
  medline-own    = {NLM},
  medline-pl     = {ENGLAND},
  medline-pmid   = {9054979},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Blood Proteins) ; 0 (Macromolecular Substances) ; 0
                   (Nitrogen Isotopes) ; 0 (Phosphoproteins) ; 0
                   (Recombinant Proteins) ; 0 (platelet protein P47) ; EC
                   3.6.1.- (GTP Phosphohydrolases) ; EC 3.6.1.50
                   (Dynamins)},
  medline-sb     = {IM},
  medline-so     = {J Mol Biol 1997 Feb 14;266(1):173-94.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=9054979},
  year           = 1997,
  doi            = {10.1006/jmbi.1996.0771}
}

@Article{Fushman98,
  author = {Fushman, David and Tjandra, Nico and Cowburn, David},
  title = {Direct Measurement of 15{N} Chemical Shift Anisotropy in Solution},
  journal = jacs,
  volume = {120},
  number = {42},
  pages = {10947-10952},
  year = {1998},
  doi = {10.1021/ja981686m},
  URL = {http://pubs.acs.org/doi/abs/10.1021/ja981686m},
  eprint = {http://pubs.acs.org/doi/pdf/10.1021/ja981686m},
  abstract = { The magnitude and orientation of the 15N chemical shift anisotropy (CSA) tensors are determined for human ubiquitin in solution from 15N relaxation data at 600, 500, and 360 MHz. The analysis uses the model-independent approach [Fushman, D.; Cowburn, D. J. Am. Chem. Soc. 1998, 120, 7109-10] based on a ratio, $\eta$/R2, of the cross correlation ($\eta$) between 15N CSA and 15N-1H dipolar interaction and of the rate (R2) of 15N transverse relaxation. Since the $\eta$/R2 ratio does not contain any direct dependence on protein dynamics, the present approach is free from assumptions about overall and local motions. The 15N CSA values fall in the range -125 to -216 ppm, with the average value of -157 $\pm$ 19 ppm; the average angle between the NH bond and the unique principal axis of the 15N CSA tensor was 15.7 $\pm$ 5.0$^\circ$ (range 6-26$^\circ$). The results indicate the importance of residue-specific 15N CSA for accurate analysis of dynamics from relaxation data, and provide access to the CSA in solution, which may be structurally useful. }
}

@Article{Fushman99,
  author = {Fushman, D. and Tjandra, N. and Cowburn, D.},
  title = {An Approach to Direct Determination of Protein Dynamics from {15N} {NMR} Relaxation at Multiple Fields, Independent of Variable {15N} Chemical Shift Anisotropy and Chemical Exchange Contributions},
  journal = jacs,
  volume = {121},
  number = {37},
  pages = {8577-8582},
  year = {1999},
  doi = {10.1021/ja9904991},
  URL = {http://pubs.acs.org/doi/abs/10.1021/ja9904991},
  eprint = {http://pubs.acs.org/doi/pdf/10.1021/ja9904991},
  abstract = { An approach to protein dynamics analysis from 15N relaxation data is demonstrated, based on multiple-field relaxation data. This provides a direct, residue-specific determination of both the spectral density components, the 15N chemical shift anisotropy (CSA) and the conformational exchange contribution to the 15N line width. Measurements of R1, R2, and 15N{1H} NOE are used. The approach is free from any assumption about the values of the CSA or of the conformational exchange. Using this approach, the spectral densities, the values of 15N CSA, and the conformational exchange contribution to the 15N line width are directly determined from the relaxation data for human ubiquitin, collected at 360, 500, and 600 MHz. The spectral densities are analyzed in terms of the order parameter and the correlation time of local motion, using an axially symmetric overall rotational diffusion model. The residue-specific values of 15N CSA and the spectral densities obtained using this approach are in agreement with those derived previously [Fushman, Tjandra, and Cowburn. J. Am. Chem. Soc. 1998, 120, 10947−10952] from CSA/dipolar cross-correlation analysis. Accurate determination of spectral densities and order parameters from 15N relaxation may be accomplished by analysis of multiple-field data without assumption of constant CSA or zero chemical exchange contributions. }
}

@Article{Gagne98,
  Author         = {Gagn{\'e}, S. M. and Tsuda, S. and Spyracopoulos, L.
                   and Kay, L. E. and Sykes, B. D.},
  Title          = {Backbone and methyl dynamics of the regulatory domain
                   of troponin {C}: anisotropic rotational diffusion and
                   contribution of conformational entropy to calcium
                   affinity.},
  Journal        = jmb,
  Volume         = {278},
  Number         = {3},
  Pages          = {667-686},
  abstract       = {The N-terminal domain (residues 1 to 90) of chicken
                   skeletal troponin C (NTnC) regulates muscle contraction
                   upon the binding of a calcium ion to each of its two
                   calcium binding loops. In order to characterize the
                   backbone dynamics of NTnC in the apo state (NTnC-apo),
                   we measured and carefully analyzed 15N NMR relaxation
                   parameters T1, T2 and NOE at 1H NMR frequencies of 500
                   and 600 MHz. The overall rotational correlation time of
                   NTnC-apo at 29.6 degrees C is 4.86 (+/-0.15) ns. The
                   experimental data indicate that the rotational
                   diffusion of NTnC-apo is anisotropic with a diffusion
                   anisotropy, D parallel/D perpendicular, of 1.10.
                   Additionally, the dynamic properties of side-chains
                   having a methyl group were derived from 2H relaxation
                   data of CH2D groups of a partially deuterated
                   sample.Based on the dynamic characteristics of TnC, two
                   different levels of "fine tuning" of the calcium
                   affinity are presented. Significantly lower backbone
                   order parameters (S2), were observed for calcium
                   binding site I relative to site II and the contribution
                   of the bond vector fluctuations to the conformational
                   entropy of sites I and II was calculated. The
                   conformational entropy loss due to calcium binding
                   (DeltaDeltaSp) differs by 1 kcal/mol between sites I
                   and II. This is consistent with the different
                   dissociation constants previously measured for sites I
                   and II of 16 microM and 1. 7 microM, respectively.In
                   addition to the direct role of binding loop dynamics,
                   the side-chain methyl group dynamics play an indirect
                   role through the energetics of the calcium-induced
                   structural change from a closed to an open state. Our
                   results show that the side-chains which will be exposed
                   upon calcium binding have reduced motion in the apo
                   state, suggesting that conformational entropic
                   contributions can be used to offset the free energy
                   cost of exposing hydrophobic groups. It is clear from
                   this work that a complete determination of their
                   dynamic characteristics is necessary in order to fully
                   understand how TnC and other proteins are fine tuned to
                   appropriately carry out their function.},
  authoraddress  = {Medical Research Council Group in Protein Structure
                   and Function, University of Alberta, Edmonton, T6G 2H7,
                   Canada.},
  keywords       = {Animals ; Apoproteins/chemistry ; Calcium/*metabolism
                   ; Chickens ; Cloning, Molecular ; Diffusion ; Entropy ;
                   Models, Chemical ; Models, Molecular ; Muscle,
                   Skeletal/metabolism ; Nuclear Magnetic Resonance,
                   Biomolecular ; *Protein Conformation ; Recombinant
                   Proteins/chemistry/metabolism ; Research Support,
                   Non-U.S. Gov't ; Rotation ; Troponin
                   C/*chemistry/*metabolism},
  language       = {eng},
  medline-aid    = {S0022283698917235 [pii]},
  medline-ci     = {Copyright 1998 Academic Press Limited.},
  medline-da     = {19980616},
  medline-dcom   = {19980616},
  medline-edat   = {1998/06/20},
  medline-fau    = {Gagne, S M ; Tsuda, S ; Spyracopoulos, L ; Kay, L E ;
                   Sykes, B D},
  medline-is     = {0022-2836},
  medline-jid    = {2985088R},
  medline-lr     = {20041117},
  medline-mhda   = {1998/06/20 00:01},
  medline-own    = {NLM},
  medline-pl     = {ENGLAND},
  medline-pmid   = {9600847},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Apoproteins) ; 0 (Recombinant Proteins) ; 0
                   (Troponin C) ; 7440-70-2 (Calcium)},
  medline-sb     = {IM},
  medline-so     = {J Mol Biol 1998 May 8;278(3):667-86.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=9600847},
  year           = 1998
}

@Book{GMW81,
  Author         = {Gill, P. E. and Murray, W. and Wright, M. H.},
  Title          = {Practical Optimization},
  Publisher      = {Academic Press},
  year           = 1981
}

@Article{Gitti05,
  Author         = {Gitti, R.K. and Wright, N.T. and Margolis, J.W. and
                   Varney, K.M. and Weber, D.J. and Margolis, F.L.},
  Title          = {Backbone dynamics of the olfactory marker protein as
                   studied by 15{N} {NMR} relaxation measurements.},
  Journal        = biochem,
  Volume         = {44},
  Number         = {28},
  Pages          = {9673-9679},
  abstract       = {Nuclear magnetic resonance (NMR) (15)N relaxation
                   measurements of the olfactory marker protein (OMP)
                   including longitudinal relaxation (T(1)), transverse
                   relaxation (T(2)), and (15)N-(1)H NOE data were
                   collected at low protein concentrations (<or=100
                   microM) and at two field strengths (14.4 and 18.8 T)
                   for 135 of 162 backbone amide groups. Rotational
                   diffusion of the OMP was found to be axially symmetric
                   with D( parallel)/D( perpendicular) = 1.20 +/- 0.02
                   with an overall global correlation time of 8.93 +/-
                   0.03 ns. Model-free internal dynamic analyses of these
                   data provided a description of the protein's dynamics
                   on multiple time scales. The results of these studies
                   indicate that there is a large degree of conformational
                   flexibility for alpha-helix 1 (alpha1), loop 1, and the
                   conserved Omega-loop (loop 3). The functional
                   significance that these dynamic regions of OMP have in
                   modulating olfactory signal transduction is discussed.},
  authoraddress  = {Department of Biochemistry and Molecular Biology,
                   University of Maryland School of Medicine, 108 North
                   Greene Street, Baltimore, Maryland 21201, USA.},
  keywords       = {Animals ; Anisotropy ; Models, Molecular ; Nerve
                   Tissue Proteins/*chemistry/physiology ; Nitrogen
                   Isotopes ; Nuclear Magnetic Resonance,
                   Biomolecular/methods ; Olfactory Marker Protein ;
                   Protein Conformation ; Protein Structure, Secondary ;
                   Rats ; Research Support, N.I.H., Extramural ; Research
                   Support, U.S. Gov't, P.H.S. ; Signal
                   Transduction/physiology ; Solutions ; *Thermodynamics},
  language       = {eng},
  doi            = {10.1021/bi050149t},
  medline-aid    = {10.1021/bi050149t [doi]},
  medline-da     = {20050712},
  medline-dcom   = {20051011},
  medline-edat   = {2005/07/13 09:00},
  medline-fau    = {Gitti, Rossitza K ; Wright, Nathan T ; Margolis, Joyce
                   W ; Varney, Kristen M ; Weber, David J ; Margolis,
                   Frank L},
  medline-gr     = {DC03112/DC/NIDCD ; DC04752/DC/NIDCD ; GM58888/GM/NIGMS},
  medline-is     = {0006-2960 (Print)},
  medline-jid    = {0370623},
  medline-jt     = {Biochemistry.},
  medline-lr     = {20051117},
  medline-mhda   = {2005/10/12 09:00},
  medline-own    = {NLM},
  medline-pl     = {United States},
  medline-pmid   = {16008352},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Nerve Tissue Proteins) ; 0 (Nitrogen Isotopes) ; 0
                   (Olfactory Marker Protein) ; 0 (Omp protein, rat) ; 0
                   (Solutions)},
  medline-sb     = {IM},
  medline-so     = {Biochemistry. 2005 Jul 19;44(28):9673-9.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=16008352},
  year           = 2005
}

@Article{Goldfarb70,
  Author         = {Goldfarb, D.},
  Title          = {A family of variable-metric methods derived by
                   variational means},
  Journal        = mc,
  Volume         = {24},
  Number         = {109},
  Pages          = {23-26},
  address        = {201 CHARLES ST, PROVIDENCE, RI 02940-2213},
  citedref       = {BROYDEN CG, 1967, MATH COMPUT, V21, P368 ; DAVIDON WC,
                   1959, ANL5990 AEC RES DEV ; DAVIDON WC, 1968, MATH
                   COMPUT, V10, P406 ; DAVIDSON WC, TID4500 ; FLETCHER R,
                   1963, MATH COMPUT, V6, P163 ; GOLDFARB D, 1968 P C OPT
                   U KEEL ; GREENSTADT J, 1970, MATH COMPUT, V24, P1 ;
                   WOLFE P, 1967, ANOTHER VARIABLE MET},
  isifile-dt     = {Article},
  isifile-ga     = {G5602},
  isifile-j9     = {MATH COMPUT},
  isifile-nr     = {8},
  isifile-pi     = {PROVIDENCE},
  isifile-sc     = {Mathematics, Applied},
  isifile-tc     = {526},
  issn           = {0025-5718},
  language       = {English},
  publisher      = {AMER MATHEMATICAL SOC},
  size           = {0 p.},
  sourceid       = {ISI:A1970G560200003},
  doi            = {10.1090/s0025-5718-1970-0258249-6},
  year           = 1970
}

@Article{Habazettl96,
  Author         = {Habazettl, J. and Myers, L. C. and Yuan, F. and
                   Verdine, G. L. and Wagner, G.},
  Title          = {Backbone dynamics, amide hydrogen exchange, and
                   resonance assignments of the {DNA}
                   methylphosphotriester repair domain of {E}scherichia
                   coli {A}da using {NMR}.},
  Journal        = biochem,
  Volume         = {35},
  Number         = {29},
  Pages          = {9335-9348},
  abstract       = {The 10kDa amino-terminal fragment of Escherichia coli
                   Ada protein (N-Ada10) repairs methyl phosphotriesters
                   in DNA and possesses a tightly bound zinc ion. The
                   complete resonance assignments of this protein domain
                   have been obtained using multidimensional homonuclear
                   and heteronuclear NMR experiments. The assignments
                   served to study the internal mobility of this protein
                   domain via 15N relaxation experiments. This involved
                   the measurement of longitudinal and transverse 15N
                   relaxation rates, as well as the amide proton solvent
                   exchange rates. Relaxation rates in the rotating frame,
                   R1 rho, of 15N nuclei were measured at different
                   spin-lock field strengths, leading to the detection of
                   two slow conformational exchange processes at Gly-25
                   and Gln-73. For the latter, which is next to the active
                   site of this protein domain, the characteristic time of
                   this process was found to be around 60 microseconds.
                   The other relaxation experiments unveiled some regions
                   of fast internal motions, faster than the overall
                   correlation time. These motions were found in the N-
                   and C- terminal tails, in segment 33-35 which forms the
                   turn between beta-strands S1 and S2, and residues 47-52
                   located in a long loop preceding strand S3. The latter
                   loop belongs to the potential DNA binding surface of
                   N-Ada10. While the structure from residue 18 to residue
                   26 appears not well defined in the calculated
                   structure, the relaxation experiments do not indicate
                   higher mobility for this region. Residues at the
                   N-terminal portion, including the first helix, the
                   sequentially adjacent loop, and part of the second
                   helix, exhibit internal motions close to the time scale
                   of the overall rotational correlation time. This
                   appears to be related to the fact that the first helix
                   has no hydrogen bonds or salt bridges to the rest of
                   the protein and is stabilized only by the involvement
                   of some of its side chains in a hydrophobic core
                   consisting of the side chains of two phenylalanines, a
                   tryptophan, a leucine, and a valine. The four cysteines
                   which bind the zinc show motions on different time
                   scales ranging from microseconds to picoseconds. Thus
                   the motions in the immediate region around the bound
                   zinc of the DNA methyl phosphotriester repair domain
                   are of relatively small amplitude but take place over a
                   wide time range. On the other hand, high mobility is
                   found in the turn connecting S1 and S2 and in the loop
                   preceding S3, regions of the potential DNA binding
                   surface.},
  authoraddress  = {Department of Biological Chemistry and Molecular
                   Pharmacology, Harvard Medical School, Boston,
                   Massachusetts 02115, USA.},
  keywords       = {Bacterial Proteins/*chemistry/metabolism ; Binding
                   Sites ; Cysteine/chemistry/metabolism ; *DNA Repair ;
                   Escherichia coli ; *Escherichia coli Proteins ;
                   Hydrogen/metabolism ; Magnetic Resonance Spectroscopy ;
                   Models, Molecular ; Peptide Fragments/chemistry ;
                   Protein Conformation ; Protein Structure, Secondary ;
                   Research Support, Non-U.S. Gov't ; Research Support,
                   U.S. Gov't, Non-P.H.S. ; Zinc/metabolism},
  language       = {eng},
  doi            = {10.1021/bi952524v},
  medline-aid    = {10.1021/bi952524v [doi] ; bi952524v [pii]},
  medline-da     = {19960916},
  medline-dcom   = {19960916},
  medline-edat   = {1996/07/23},
  medline-fau    = {Habazettl, J ; Myers, L C ; Yuan, F ; Verdine, G L ;
                   Wagner, G},
  medline-is     = {0006-2960},
  medline-jid    = {0370623},
  medline-lr     = {20041117},
  medline-mhda   = {1996/07/23 00:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {8755711},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Ada protein, E coli) ; 0 (Bacterial Proteins) ; 0
                   (Escherichia coli Proteins) ; 0 (Peptide Fragments) ;
                   1333-74-0 (Hydrogen) ; 52-90-4 (Cysteine) ; 7440-66-6
                   (Zinc)},
  medline-sb     = {IM},
  medline-so     = {Biochemistry 1996 Jul 23;35(29):9335-48.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=8755711},
  year           = 1996
}

@Article{Hansen08,
  Author         = {Hansen, D. F. and Vallurupalli, P. and Lundstrom, P.
                   and Neudecker, P. and Kay, L. E.},
  Title          = {Probing chemical shifts of invisible states of
                   proteins with relaxation dispersion {NMR} spectroscopy:
                   how well can we do?},
  Journal        = jacs,
  Volume         = {130},
  Number         = {8},
  Pages          = {2667-2675},
  abstract       = {Carr-Purcell-Meiboom-Gill relaxation dispersion NMR
                   spectroscopy has evolved into a powerful approach for
                   the study of low populated, invisible conformations of
                   biological molecules. One of the powerful features of
                   the experiment is that chemical shift differences
                   between the exchanging conformers can be obtained,
                   providing structural information about invisible
                   excited states. Through the development of new labeling
                   approaches and NMR experiments it is now possible to
                   measure backbone 13C(alpha) and 13CO relaxation
                   dispersion profiles in proteins without complications
                   from 13C-13C couplings. Such measurements are presented
                   here, along with those that probe exchange using 15N
                   and 1HN nuclei. A key experimental design has been the
                   choice of an exchanging system where excited-state
                   chemical shifts were known from independent
                   measurement. Thus it is possible to evaluate
                   quantitatively the accuracy of chemical shift
                   differences obtained in dispersion experiments and to
                   establish that in general very accurate values can be
                   obtained. The experimental work is supplemented by
                   computations that suggest that similarly accurate
                   shifts can be measured in many cases for systems with
                   exchange rates and populations that fall within the
                   range of those that can be quantified by relaxation
                   dispersion. The accuracy of the extracted chemical
                   shifts opens up the possibility of obtaining
                   quantitative structural information of invisible states
                   of the sort that is now available from chemical shifts
                   recorded on ground states of proteins.},
  authoraddress  = {Department of Medical Genetics, University of Toronto,
                   Toronto, Ontario, Canada, M5S 1A8.},
  doi            = {10.1021/ja078337p},
  keywords       = {Computer Simulation ; Magnetic Resonance
                   Spectroscopy/*methods/*standards ; Microfilament
                   Proteins/*chemistry ; Protein Conformation ; Protein
                   Folding ; Protein-Serine-Threonine Kinases/*chemistry ;
                   Reference Standards ; Saccharomyces cerevisiae
                   Proteins/*chemistry},
  language       = {eng},
  medline-aid    = {10.1021/ja078337p [doi]},
  medline-crdt   = {2008/02/02 09:00},
  medline-da     = {20080220},
  medline-dcom   = {20080415},
  medline-dep    = {20080201},
  medline-edat   = {2008/02/02 09:00},
  medline-fau    = {Hansen, D Flemming ; Vallurupalli, Pramodh ;
                   Lundstrom, Patrik ; Neudecker, Philipp ; Kay, Lewis E},
  medline-is     = {1520-5126 (Electronic) ; 0002-7863 (Linking)},
  medline-jid    = {7503056},
  medline-jt     = {Journal of the American Chemical Society},
  medline-lid    = {10.1021/ja078337p [doi]},
  medline-mhda   = {2008/04/16 09:00},
  medline-own    = {NLM},
  medline-phst   = {2008/02/01 [aheadofprint]},
  medline-pl     = {United States},
  medline-pmid   = {18237174},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article ; Research Support, Non-U.S. Gov't},
  medline-rn     = {0 (ABP1 protein, S cerevisiae) ; 0 (Microfilament
                   Proteins) ; 0 (Saccharomyces cerevisiae Proteins) ; EC
                   2.7.1.- (ARK1 protein, S cerevisiae) ; EC 2.7.11.1
                   (Protein-Serine-Threonine Kinases)},
  medline-sb     = {IM},
  medline-so     = {J Am Chem Soc. 2008 Feb 27;130(8):2667-75. doi:
                   10.1021/ja078337p. Epub 2008 Feb 1.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=18237174},
  year           = 2008
}

@Article{HestenesStiefel52,
  Author         = {Hestenes, M. R. and Stiefel, E.},
  Title          = {Methods of conjugate gradients for solving linear
                   systems},
  Journal        = jrnbs,
  Volume         = {49},
  Number         = {6},
  Pages          = {409-436},
  address        = {SUPERINTENDENT DOCUMENTS, WASHINGTON, DC 20402-9325},
  citedref       = {FOX, 1948, Q J MECHANICS APPLIE, P149 ; HESTENES MR,
                   1951, NAML529 NBS REP ; HOCHSTRASSER U, THESIS ETH
                   ZURICH ; LANCZOS C, 1950, J RES NAT BUR STAN B, V45,
                   P255 ; LANCZOS C, 1951, 2ND P S LARG SCAL DI, P164 ;
                   LANCZOS C, 1951, NAML5213 NBS REP ; ROSSER JB, 1951,
                   UNPUB AUG S SIM LIN ; STIEFEL E, 1951, UNPUB AUG S SIM
                   LIN ; STIEFEL E, 1952, Z ANGEW MATH PHYSIK ; SZEGO G,
                   1939, AM MATH SOC C PUBLIC, V23 ; WALL HS, 1948, ANAL
                   THEORY CONTINUE},
  isifile-dt     = {Article},
  isifile-ga     = {UN385},
  isifile-j9     = {J RES NAT BUR STAND},
  isifile-nr     = {11},
  isifile-pi     = {WASHINGTON},
  isifile-sc     = {Engineering, Multidisciplinary},
  isifile-tc     = {1180},
  language       = {English},
  publisher      = {US GOVERNMENT PRINTING OFFICE},
  size           = {28 p.},
  sourceid       = {ISI:A1952UN38500008},
  doi            = {10.6028/jres.049.044},
  year           = 1952
}

@Article{Horne07,
  Author         = {Horne, J. and d'Auvergne, E.J. and Coles, M. and
                   Velkov, T. and Chin, Y. and Charman, W.N. and Prankerd,
                   R. and Gooley, P.R. and Scanlon, M.J.},
  Title          = {Probing the flexibility of the {D}sb{A} oxidoreductase
                   from {V}ibrio cholerae--a 15{N} - 1{H} heteronuclear
                   {NMR} relaxation analysis of oxidized and reduced forms
                   of {D}sb{A}.},
  Journal        = jmb,
  Volume         = {371},
  Number         = {3},
  Pages          = {703-716},
  abstract       = {We have determined the structure of the reduced form
                   of the DsbA oxidoreductase from Vibrio cholerae. The
                   reduced structure shows a high level of similarity to
                   the crystal structure of the oxidized form and is
                   typical of this class of enzyme containing a
                   thioredoxin domain with an inserted alpha-helical
                   domain. Proteolytic and thermal stability measurements
                   show that the reduced form of DsbA is considerably more
                   stable than the oxidized form. NMR relaxation data have
                   been collected and analyzed using a model-free approach
                   to probe the dynamics of the reduced and oxidized
                   states of DsbA. Akaike's information criteria have been
                   applied both in the selection of the model-free models
                   and the diffusion tensors that describe the global
                   motions of each redox form. Analysis of the dynamics
                   reveals that the oxidized protein shows increased
                   disorder on the pico- to nanosecond and micro- to
                   millisecond timescale. Many significant changes in
                   dynamics are located either close to the active site or
                   at the insertion points between the domains. In
                   addition, analysis of the diffusion data shows there is
                   a clear difference in the degree of interdomain
                   movement between oxidized and reduced DsbA with the
                   oxidized form being the more rigid. Principal
                   components analysis has been employed to indicate
                   possible concerted movements in the DsbA structure,
                   which suggests that the modeled interdomain motions
                   affect the catalytic cleft of the enzyme. Taken
                   together, these data provide compelling evidence of a
                   role for dynamics in the catalytic cycle of DsbA.},
  authoraddress  = {Department of Medicinal Chemistry, Victorian College
                   of Pharmacy, Monash University, 381 Royal Parade,
                   Parkville, VIC 3052, Australia.},
  keywords       = {Amino Acid Sequence ; Catalytic Domain ;
                   Crystallography, X-Ray ; Diffusion ; Enzyme Stability ;
                   Hydrogen ; Models, Molecular ; Molecular Sequence Data
                   ; Nitrogen Isotopes ; *Nuclear Magnetic Resonance,
                   Biomolecular ; Oxidation-Reduction ; *Pliability ;
                   Protein Disulfide-Isomerase/*chemistry ; Protein
                   Structure, Secondary ; Vibrio cholerae/*enzymology},
  language       = {eng},
  doi            = {10.1016/j.jmb.2007.05.067},
  medline-aid    = {S0022-2836(07)00707-3 [pii] ;
                   10.1016/j.jmb.2007.05.067 [doi]},
  medline-da     = {20070730},
  medline-dcom   = {20070927},
  medline-dep    = {20070531},
  medline-edat   = {2007/06/26 09:00},
  medline-fau    = {Horne, James ; d'Auvergne, Edward J ; Coles, Murray ;
                   Velkov, Tony ; Chin, Yanni ; Charman, William N ;
                   Prankerd, Richard ; Gooley, Paul R ; Scanlon, Martin J},
  medline-is     = {0022-2836 (Print)},
  medline-jid    = {2985088R},
  medline-jt     = {Journal of molecular biology},
  medline-mhda   = {2007/09/28 09:00},
  medline-own    = {NLM},
  medline-phst   = {2006/12/11 [received] ; 2007/04/18 [revised] ;
                   2007/05/21 [accepted] ; 2007/05/31 [aheadofprint]},
  medline-pl     = {England},
  medline-pmid   = {17585933},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article ; Research Support, Non-U.S. Gov't},
  medline-pubm   = {Print-Electronic},
  medline-rn     = {0 (Nitrogen Isotopes) ; 1333-74-0 (Hydrogen) ; EC
                   5.3.4.1 (Protein Disulfide-Isomerase)},
  medline-sb     = {IM},
  medline-si     = {PDB/2IJY},
  medline-so     = {J Mol Biol. 2007 Aug 17;371(3):703-16. Epub 2007 May
                   31.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=17585933},
  year           = 2007
}

@Article{Hubbard69,
  Author         = {Hubbard, P. S.},
  Title          = {Some properties of correlation functions of
                   irreducible tensor operators},
  Journal        = physrev,
  Volume         = {180},
  Number         = {1},
  Pages          = {319-326},
  address        = {One Physics Ellipse, College PK, MD 20740-3844 USA},
  citedref       = {ABRAGAM A, 1961, PRINCIPLES NUCLEAR M, P313 ; BRINK
                   DM, 1962, ANGULAR MOMENTUM ; BRINK DM, 1962, ANGULAR
                   MOMENTUM, P59 ; GORDON RG, 1968, ADVANCES MAGNETIC RE,
                   V3 ; HUBBARD PS, 1961, REV MOD PHYS, V33, P249 ;
                   HUBBARD PS, 1963, PHYS REV, V131, P1155 ; RAMSEY N,
                   1963, MOL BEAMS, CH3 ; ROSE ME, 1957, ELEMENTARY THEORY
                   AN ; WAUGH JS, 1968, ADVANCES MAGNETIC ED, V3},
  isifile-dt     = {Article},
  isifile-ga     = {D3383},
  isifile-j9     = {Phys Rev},
  isifile-nr     = {9},
  isifile-pi     = {College PK},
  isifile-sc     = {Physics, Multidisciplinary},
  isifile-tc     = {100},
  issn           = {0031-899X},
  language       = {English},
  publisher      = {American Physical Soc},
  size           = {0 p.},
  sourceid       = {ISI:A1969D338300040},
  year           = 1969
}

@Article{Huntress68,
  Author         = {Huntress, W. T.},
  Title          = {Effects of anisotropic molecular rotational diffusion
                   on nuclear magnetic relaxation in liquids},
  Journal        = jcp,
  Volume         = {48},
  Number         = {8},
  Pages          = {3524-3533},
  address        = {Circulation Fulfillment Div, 500 Sunnyside Blvd,
                   Woodbury, NY 11797-2999},
  citedref       = {ABRAGAM A, 1961, PRINCIPLES NUCLEAR M ; BLOEMBERGEN N,
                   1948, PHYS REV, V73, P679 ; BOPP TT, 1967, J CHEM PHYS,
                   V47, P3621 ; EISNER M, 1961, B AM PHYS SOC, V6, P363 ;
                   FAVRO LD, 1960, PHYS REV, V119, P53 ; FREED JH, 1964, J
                   CHEM PHYS, V41, P2077 ; MITCHELL RW, 1960, J CHEM PHYS,
                   V33, P86 ; MITCHELL RW, 1961, J CHEM PHYS, V34, P651 ;
                   MONIZ WB, 1963, J CHEM PHYS, V38, P1155 ; MONIZ WB,
                   1963, J CHEM PHYS, V38, P2418 ; OREILLY RE, 1963, J
                   CHEM PHYS, V39, P1768 ; POWLES JG, 1966, MOL PHYS, V10,
                   P155 ; ROSE ME, 1957, ELEMENTARY THEORY AN ; SHIMIZU H,
                   1962, J CHEM PHYS, V37, P765 ; SHIMIZU H, 1964, J CHEM
                   PHYS, V40, P754 ; TOWNES CH, 1955, MICROWAVE SPECTROSCO
                   ; VALIEV KA, 1962, SOV PHYS JETP, V15, P353 ; WIGNER E,
                   1959, GROUP THEORY ITS APP ; WOESSNER DE, 1962, J CHEM
                   PHYS, V37, P647 ; WOESSNER DE, 1964, J CHEM PHYS, V40,
                   P2341 ; ZWANZIG R, 1965, ANNU REV PHYS CHEM, V16, P67},
  isifile-dt     = {Article},
  isifile-ga     = {B3401},
  isifile-j9     = {J Chem Phys},
  isifile-ji     = {J. Chem. Phys.},
  isifile-nr     = {21},
  isifile-pi     = {Woodbury},
  isifile-sc     = {Physics, Atomic, Molecular \& Chemical},
  isifile-tc     = {312},
  issn           = {0021-9606},
  language       = {English},
  publisher      = {Amer Inst Physics},
  size           = {0 p.},
  sourceid       = {ISI:A1968B340100023},
  year           = 1968
}

@Article{HurvichTsai89,
  Author         = {Hurvich, C. M. and Tsai, C. L.},
  Title          = {Regression and time-series model selection in small
                   samples},
  Journal        = biometrika,
  Volume         = {76},
  Number         = {2},
  Pages          = {297-307},
  address        = {Univ College London Gower St-Biometrika Office,
                   London, England WC1E 6BT},
  authoraddress  = {Univ Calif Davis,Div Stat,Davis,CA 95616.},
  citedref       = {AKAIKE H, 1970, ANN I STATISTICAL MA, V22, P203 ;
                   AKAIKE H, 1973, 2 INT S INF THEOR, P267 ; AKAIKE H,
                   1978, ANN I STAT MATH, V30, P9 ; ALLEN DM, 1974,
                   TECHNOMETRICS, V16, P125 ; BHANSALI RJ, 1977,
                   BIOMETRIKA, V64, P547 ; BHANSALI RJ, 1986, ANN STAT,
                   V14, P315 ; BROCKWELL PJ, 1987, TIME SERIES THEORY M ;
                   BURG JP, 1978, MODERN SPECTRUM ANAL, P42 ; GALLANT AR,
                   1986, NONLINEAR STATISTICA ; HANNAN EJ, 1979, J ROY
                   STAT SOC B MET, V41, P190 ; HANNAN EJ, 1980, ANN STAT,
                   V8, P1071 ; JOHNSON NL, 1970, CONTINUOUS UNIVARIAT, V1
                   ; LINHART H, 1986, MODEL SELECTION ; MALLOWS CL, 1973,
                   TECHNOMETRICS, V12, P591 ; PARZEN E, 1977, MULTIVARIATE
                   ANAL, V4, P283 ; PRIESTLEY MB, 1981, SPECTRAL ANAL TIME
                   S ; SCHWARZ G, 1978, ANN STAT, V6, P461 ; SHIBATA R,
                   1976, BIOMETRIKA, V63, P117 ; SHIBATA R, 1980, ANN
                   STAT, V8, P147 ; SHIBATA R, 1981, BIOMETRIKA, V68, P45
                   ; SHIBATA R, 1986, J APPL PROBAB A, V23, P127 ; SUGIURA
                   N, 1978, COMMUNICATIONS STA A, V7, P13 ; TSAY RS, 1984,
                   ANN STAT, V12, P1425 ; WHITTLE P, 1953, J ROY STAT SOC
                   B MET, V15, P125},
  isifile-dt     = {Article},
  isifile-ga     = {AE134},
  isifile-j9     = {Biometrika},
  isifile-ji     = {Biometrika},
  isifile-nr     = {24},
  isifile-pi     = {London},
  isifile-rp     = {Hurvich, CM, NYU,Dept Stat \& Operat Res,New York,NY
                   10003.},
  isifile-sc     = {Mathematics, Interdisciplinary Applications; Biology;
                   Statistics \& ; Probability},
  isifile-tc     = {304},
  issn           = {0006-3444},
  language       = {English},
  month          = {Jun},
  publisher      = {Biometrika Trust},
  size           = {11 p.},
  sourceid       = {ISI:A1989AE13400012},
  doi            = {10.1093/biomet/76.2.297},
  year           = 1989
}

@Article{IshimaTorchia99,
  Author         = {Ishima, R. and Torchia, D.A.},
  Title          = {Estimating the time scale of chemical exchange of
                   proteins from measurements of transverse relaxation
                   rates in solution},
  Journal        = jbnmr,
  Volume         = {14},
  Number         = {4},
  Pages          = {369-372},
  abstract       = {Chemical (conformational) exchange on the ms-mu s
                   time scale is reliably identified by the observation of
                   transverse relaxation rates, R-ex, that depend upon the
                   strength of the effective field (omega(1eff) = gamma
                   B-1eff) used in spin lock or CPMG experiments. In order
                   to determine if the exchange correlation time, tau(ex),
                   is the fast or slow limit, measurements of (i) signal
                   line shape and (ii) temperature dependence of R-ex have
                   been commonly used in studies of stable, small
                   molecules. However, these approaches are often not
                   applicable to proteins, because sample stability and
                   solubility, respectively, limit the temperature range
                   and signal sensitivity of experiments. Herein we use a
                   complex, but general, two-site exchange equation to
                   show when the simple fast exchange equations for R-ex
                   are good approximations, in the case of proteins. We
                   then present a simple empirical equation that
                   approximately predicts R-ex in all exchange regimes,
                   and explains these results in a clear, straightforward
                   manner. Finally we show how one can reliably determine
                   whether tau(ex) is in the fast or slow exchange limit.},
  address        = {SPUIBOULEVARD 50, PO BOX 17, 3300 AA DORDRECHT,
                   NETHERLANDS},
  affiliation    = {Torchia, DA (Reprint Author), Natl Inst Dent \&
                   Craniofacial Res, Struct Mol Biol Unit, NIH, Bethesda,
                   MD 20892 USA. Natl Inst Dent \& Craniofacial Res,
                   Struct Mol Biol Unit, NIH, Bethesda, MD 20892 USA.},
  doc-delivery-number = {234VK},
  doi            = {10.1023/A:1008324025406},
  issn           = {0925-2738},
  journal-iso    = {J. Biomol. NMR},
  keywords       = {chemical exchange; protein; relaxation},
  keywords-plus  = {N-15},
  language       = {English},
  month          = {AUG},
  number-of-cited-references = {15},
  publisher      = {KLUWER ACADEMIC PUBL},
  research-areas = {Biochemistry \& Molecular Biology; Spectroscopy},
  times-cited    = {58},
  type           = {Article},
  unique-id      = {ISI:000082504900007},
  web-of-science-categories = {Biochemistry \& Molecular Biology; Spectroscopy},
  year           = 1999
}

@Article{IshimaTorchia05,
  Author         = {Ishima, R. and Torchia, D. A.},
  Title          = {Error estimation and global fitting in
                   transverse-relaxation dispersion experiments to
                   determine chemical-exchange parameters.},
  Journal        = jbnmr,
  Volume         = {32},
  Number         = {1},
  Pages          = {41-54},
  abstract       = {Off-resonance effects can introduce significant
                   systematic errors in R2 measurements in constant-time
                   Carr-Purcell-Meiboom-Gill (CPMG) transverse relaxation
                   dispersion experiments. For an off-resonance chemical
                   shift of 500 Hz, 15N relaxation dispersion profiles
                   obtained from experiment and computer simulation
                   indicated a systematic error of ca. 3\%. This error is
                   three- to five-fold larger than the random error in R2
                   caused by noise. Good estimates of total R2 uncertainty
                   are critical in order to obtain accurate estimates in
                   optimized chemical exchange parameters and their
                   uncertainties derived from chi2 minimization of a
                   target function. Here, we present a simple empirical
                   approach that provides a good estimate of the total
                   error (systematic + random) in 15N R2 values measured
                   for the HIV protease. The advantage of this empirical
                   error estimate is that it is applicable even when some
                   of the factors that contribute to the off-resonance
                   error are not known. These errors are incorporated into
                   a chi2 minimization protocol, in which the
                   Carver-Richards equation is used fit the observed R2
                   dispersion profiles, that yields optimized chemical
                   exchange parameters and their confidence limits.
                   Optimized parameters are also derived, using the same
                   protein sample and data-fitting protocol, from 1H R2
                   measurements in which systematic errors are negligible.
                   Although 1H and 15N relaxation profiles of individual
                   residues were well fit, the optimized exchange
                   parameters had large uncertainties (confidence limits).
                   In contrast, when a single pair of exchange parameters
                   (the exchange lifetime, tau(ex), and the fractional
                   population, p(a)), were constrained to globally fit all
                   R2 profiles for residues in the dimer interface of the
                   protein, confidence limits were less than 8\% for all
                   optimized exchange parameters. In addition, F-tests
                   showed that quality of the fits obtained using tau(ex),
                   p(a) as global parameters were not improved when these
                   parameters were free to fit the R2 profiles of
                   individual residues. Finally, nearly the same optimized
                   global tau(ex), p(a) values were obtained, when the 1H
                   and 15N data sets for residues in the dimer interface,
                   were fit independently; the difference in optimized
                   global parameters, ca. 10\%, was of marginal
                   significance according to the F-test.},
  authoraddress  = {Molecular Structural Biology Unit, National Institute
                   of Dental and Craniofacial Research, National
                   Institutes of Health, Bethesda, MD 20892-4307, USA.
                   rishima@dir.nidcr.nih.gov},
  keywords       = {*Data Interpretation, Statistical ;
                   Deuterium/chemistry ; HIV Protease/chemistry ; *Models,
                   Theoretical ; Nitrogen Isotopes/chemistry ; Nuclear
                   Magnetic Resonance, Biomolecular/*methods ;
                   Thermodynamics},
  language       = {eng},
  doi            = {10.1007/s10858-005-3593-z},
  medline-aid    = {10.1007/s10858-005-3593-z [doi]},
  medline-crdt   = {2005/07/26 09:00},
  medline-da     = {20050725},
  medline-dcom   = {20051108},
  medline-edat   = {2005/07/26 09:00},
  medline-fau    = {Ishima, Rieko ; Torchia, Dennis A},
  medline-is     = {0925-2738 (Print) ; 0925-2738 (Linking)},
  medline-jid    = {9110829},
  medline-jt     = {Journal of biomolecular NMR},
  medline-lr     = {20061115},
  medline-mhda   = {2005/11/09 09:00},
  medline-own    = {NLM},
  medline-phst   = {2004/12/17 [received] ; 2005/02/08 [accepted]},
  medline-pl     = {Netherlands},
  medline-pmid   = {16041482},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article ; Research Support, N.I.H., Intramural},
  medline-rn     = {0 (Nitrogen Isotopes) ; 7782-39-0 (Deuterium) ; EC
                   3.4.23.- (HIV Protease)},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR. 2005 May;32(1):41-54.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=16041482},
  year           = 2005
}

@Article{Jin98,
  Author         = {Jin, D. and Andrec, M. and Montelione, G. T. and Levy,
                   R. M.},
  Title          = {Propagation of experimental uncertainties using the
                   {L}ipari-{S}zabo model-free analysis of protein
                   dynamics.},
  Journal        = jbnmr,
  Volume         = {12},
  Number         = {4},
  Pages          = {471-492},
  abstract       = {In this paper we make use of the graphical procedure
                   previously described [Jin, D. et al. (1997) J. Am.
                   Chem. Soc., 119, 6923-6924] to analyze NMR relaxation
                   data using the Lipari-Szabo model-free formalism. The
                   graphical approach is advantageous in that it allows
                   the direct visualization of the experimental
                   uncertainties in the motional parameter space. Some
                   general 'rules' describing the relationship between the
                   precision of the relaxation measurements and the
                   precision of the model-free parameters and how this
                   relationship changes with the overall tumbling time
                   (tau m) are summarized. The effect of the precision in
                   the relaxation measurements on the detection of
                   internal motions not close to the extreme narrowing
                   limit is analyzed. We also show that multiple timescale
                   internal motions may be obscured by experimental
                   uncertainty, and that the collection of relaxation data
                   at very high field strength can improve the ability to
                   detect such deviations from the simple Lipari-Szabo
                   model.},
  authoraddress  = {Department of Chemistry, Wright-Rieman Laboratories,
                   Piscataway, NJ, USA.},
  keywords       = {Models, Theoretical ; Nuclear Magnetic Resonance,
                   Biomolecular/methods ; *Protein Conformation ;
                   Proteins/*chemistry ; Research Support, U.S. Gov't,
                   P.H.S.},
  language       = {eng},
  medline-da     = {19990119},
  medline-dcom   = {19990119},
  medline-edat   = {1998/12/23},
  medline-fau    = {Jin, D ; Andrec, M ; Montelione, G T ; Levy, R M},
  medline-gr     = {GM-30580/GM/NIGMS ; GM-50733/GM/NIGMS},
  medline-is     = {0925-2738},
  medline-jid    = {9110829},
  medline-lr     = {20041117},
  medline-mhda   = {1998/12/23 00:01},
  medline-own    = {NLM},
  medline-pl     = {NETHERLANDS},
  medline-pmid   = {9862126},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Proteins)},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR 1998 Nov;12(4):471-92.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=9862126},
  year           = 1998
}

@Article{Kay89,
  Author         = {Kay, L. E. and Torchia, D. A. and Bax, A.},
  Title          = {Backbone dynamics of proteins as studied by 15{N}
                   inverse detected heteronuclear {NMR} spectroscopy:
                   application to staphylococcal nuclease.},
  Journal        = biochem,
  Volume         = {28},
  Number         = {23},
  Pages          = {8972-8979},
  abstract       = {This paper describes the use of novel two-dimensional
                   nuclear magnetic resonance (NMR) pulse sequences to
                   provide insight into protein dynamics. The sequences
                   developed permit the measurement of the relaxation
                   properties of individual nuclei in macromolecules,
                   thereby providing a powerful experimental approach to
                   the study of local protein mobility. For isotopically
                   labeled macromolecules, the sequences enable
                   measurements of heteronuclear nuclear Overhauser
                   effects (NOE) and spin-lattice (T1) and spin-spin (T2)
                   15N or 13C relaxation times with a sensitivity similar
                   to those of many homonuclear 1H experiments. Because T1
                   values and heteronuclear NOEs are sensitive to
                   high-frequency motions (10(8)-10(12) s-1) while T2
                   values are also a function of much slower processes, it
                   is possible to explore dynamic events occurring over a
                   large time scale. We have applied these techniques to
                   investigate the backbone dynamics of the protein
                   staphylococcal nuclease (S. Nase) complexed with
                   thymidine 3',5'-bisphosphate (pdTp) and Ca2+ and
                   labeled uniformly with 15N. T1, T2, and NOE values were
                   obtained for over 100 assigned backbone amide nitrogens
                   in the protein. Values of the order parameter (S),
                   characterizing the extent of rapid 1H-15N bond motions,
                   have been determined. These results suggest that there
                   is no correlation between these rapid small amplitude
                   motions and secondary structure for S. Nase. In
                   contrast, 15N line widths suggest a possible
                   correlation between secondary structure and motions on
                   the millisecond time scale. In particular, the loop
                   region between residues 42 and 56 appears to be
                   considerably more flexible on this slow time scale than
                   the rest of the protein.},
  authoraddress  = {Laboratory of Chemical Physics, National Institute of
                   Diabetes and Digestive and Kidney Diseases, Bethesda,
                   Maryland 20892.},
  keywords       = {Calcium/pharmacokinetics ; Cell Nucleus/enzymology ;
                   Escherichia coli/enzymology ; Magnetic Resonance
                   Spectroscopy/methods ; *Micrococcal Nuclease ; Nitrogen
                   Isotopes ; Peptide Mapping ; Protein Conformation ;
                   Research Support, Non-U.S. Gov't ; Research Support,
                   U.S. Gov't, P.H.S. ; *Thermodynamics ; Thymine
                   Nucleotides},
  language       = {eng},
  medline-da     = {19900222},
  medline-dcom   = {19900222},
  medline-edat   = {1989/11/14},
  medline-fau    = {Kay, L E ; Torchia, D A ; Bax, A},
  medline-is     = {0006-2960},
  medline-jid    = {0370623},
  medline-lr     = {20041117},
  medline-mhda   = {1989/11/14 00:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {2690953},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Nitrogen Isotopes) ; 0 (Thymine Nucleotides) ;
                   2863-04-9 (thymidine 3',5'-diphosphate) ; 7440-70-2
                   (Calcium) ; EC 3.1.31.1 (Micrococcal Nuclease)},
  medline-sb     = {IM},
  medline-so     = {Biochemistry 1989 Nov 14;28(23):8972-9.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=2690953},
  doi            = {10.1021/bi00449a003},
  year           = 1989
}

@Article{KlecknerFoster12,
  Author         = {Kleckner, I. R. and Foster, M. P.},
  Title          = {G{UARDD}: user-friendly {MATLAB} software for rigorous
                   analysis of {CPMG} {RD} {NMR} data.},
  Journal        = jbnmr,
  Volume         = {52},
  Number         = {1},
  Pages          = {11-22},
  abstract       = {Molecular dynamics are essential for life, and nuclear
                   magnetic resonance (NMR) spectroscopy has been used
                   extensively to characterize these phenomena since the
                   1950s. For the past 15 years, the Carr-Purcell
                   Meiboom-Gill relaxation dispersion (CPMG RD) NMR
                   experiment has afforded advanced NMR labs access to
                   kinetic, thermodynamic, and structural details of
                   protein and RNA dynamics in the crucial mus-ms time
                   window. However, analysis of RD data is challenging
                   because datasets are often large and require many
                   non-linear fitting parameters, thereby confounding
                   assessment of accuracy. Moreover, novice CPMG
                   experimentalists face an additional barrier because
                   current software options lack an intuitive user
                   interface and extensive documentation. Hence, we
                   present the open-source software package GUARDD
                   (Graphical User-friendly Analysis of Relaxation
                   Dispersion Data), which is designed to organize,
                   automate, and enhance the analytical procedures which
                   operate on CPMG RD data (
                   http://code.google.com/p/guardd/). This MATLAB-based
                   program includes a graphical user interface, permits
                   global fitting to multi-field, multi-temperature,
                   multi-coherence data, and implements chi (2)-mapping
                   procedures, via grid-search and Monte Carlo methods, to
                   enhance and assess fitting accuracy. The presentation
                   features allow users to seamlessly traverse the large
                   amount of results, and the RD Simulator feature can
                   help design future experiments as well as serve as a
                   teaching tool for those unfamiliar with RD phenomena.
                   Based on these innovative features, we expect that
                   GUARDD will fill a well-defined gap in service of the
                   RD NMR community.},
  authoraddress  = {Biophysics Program, The Ohio State University, 484
                   West 12th Ave Room 776, Columbus, OH 43210, USA.
                   ian.kleckner@gmail.com},
  keywords       = {Algorithms ; Animals ; Humans ; Models, Molecular ;
                   *Molecular Dynamics Simulation ; Nuclear Magnetic
                   Resonance, Biomolecular/instrumentation/*methods ;
                   Proteins/*chemistry ; RNA/*chemistry ; *Software ;
                   Statistics as Topic/methods},
  language       = {eng},
  medline-aid    = {10.1007/s10858-011-9589-y [doi]},
  medline-crdt   = {2011/12/14 06:00},
  medline-da     = {20120126},
  medline-dcom   = {20120516},
  medline-dep    = {20111211},
  medline-edat   = {2011/12/14 06:00},
  medline-fau    = {Kleckner, Ian R ; Foster, Mark P},
  medline-gr     = {R01 GM077234/GM/NIGMS NIH HHS/United States ;
                   R01GM077234/GM/NIGMS NIH HHS/United States},
  medline-is     = {1573-5001 (Electronic) ; 0925-2738 (Linking)},
  medline-jid    = {9110829},
  medline-jt     = {Journal of biomolecular NMR},
  medline-lid    = {10.1007/s10858-011-9589-y [doi]},
  medline-lr     = {20130627},
  medline-mhda   = {2012/05/17 06:00},
  medline-mid    = {NIHMS442561},
  medline-oid    = {NLM: NIHMS442561 ; NLM: PMC3593345},
  medline-own    = {NLM},
  medline-phst   = {2011/06/29 [received] ; 2011/09/25 [accepted] ;
                   2011/12/11 [aheadofprint]},
  medline-pl     = {Netherlands},
  medline-pmc    = {PMC3593345},
  medline-pmid   = {22160811},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article ; Research Support, N.I.H., Extramural},
  medline-rn     = {0 (Proteins) ; 63231-63-0 (RNA)},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR. 2012 Jan;52(1):11-22. doi:
                   10.1007/s10858-011-9589-y. Epub 2011 Dec 11.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=22160811},
  doi            = {10.1007/s10858-011-9589-y},
  year           = 2012
}

@Article{Korzhnev01,
  Author         = {Korzhnev, D. M. and Billeter, M. and Arseniev, A. S.
                   and Orekhov, V. Y.},
  Title          = {{NMR} studies of {B}rownian tumbling and internal
                   motions in proteins},
  Journal        = pnmrs,
  Volume         = {38},
  Number         = {3},
  Pages          = {197-266},
  address        = {The Boulevard, Langford Lane, Kidlington, Oxford OX5
                   1GB, England},
  authoraddress  = {Univ Gothenburg, Swedish NMR Ctr, S-40530 Gothenburg,
                   Sweden. ; Russian Acad Sci, Shemyakin \& Ovchinikov
                   Inst Bioorgan Chem, Moscow 117871, Russia. ; Univ
                   Gothenburg, Lundberg lab, S-40530 Gothenburg, Sweden.},
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                   1970, J CHEM PHYS, V53, P436 ; YAMASAKI K, 1995,
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                   CHEM SOC, V116, P8266 ; ZARE RN, 1988, ANGULAR MOMENTUM
                   UND ; ZHANG WX, 1998, BIOCHEMISTRY-US, V37, P7119 ;
                   ZHENG Z, 1995, BIOCHEMISTRY-US, V34, P5212 ; ZHOU HX,
                   1995, BIOPHYS J, V69, P2286 ; ZINNJUSTIN S, 1997, J
                   BIOMOL NMR, V10, P363},
  isifile-dt     = {Review},
  isifile-ga     = {409GU},
  isifile-j9     = {Prog Nucl Magn Reson Spectros},
  isifile-ji     = {Prog. Nucl. Magn. Reson. Spectrosc.},
  isifile-nr     = {251},
  isifile-pi     = {Oxford},
  isifile-rp     = {Orekhov, VY, Univ Gothenburg, Swedish NMR Ctr, Box
                   465, S-40530 ; Gothenburg, Sweden.},
  isifile-sc     = {Physics, Atomic, Molecular \& Chemical; Nuclear
                   Science \& Technology; ; Spectroscopy},
  isifile-tc     = {54},
  issn           = {0079-6565},
  keywords       = {relaxation theory; cross-correlation; CSA; backbone
                   dynamics; hydrodynamics; diffusion anisotropy;
                   model-free; rotating frame; conformational exchange;
                   molecular dynamics; normal mode ; [ISI:] n-15
                   chemical-shift; nuclear-magnetic-resonance;
                   molecular-dynamics simulations; model-free approach;
                   anisotropic rotational diffusion; pulsed-field
                   gradients; coli ribonuclease hi; heteronuclear
                   relaxation experiments; studying translational
                   diffusion; spectral density-functions ;;},
  language       = {English},
  month          = {APR 20},
  publisher      = {Pergamon-Elsevier Science Ltd},
  size           = {70 p.},
  sourceid       = {ISI:000167376800001},
  doi            = {10.1016/s0079-6565(00)00028-5},
  year           = 2001
}

@Article{Korzhnev97,
  Author         = {Korzhnev, D. M. and Orekhov, V. Y. and Arseniev, A. S.},
  Title          = {Model-free approach beyond the borders of its
                   applicability.},
  Journal        = jmr,
  Volume         = {127},
  Number         = {2},
  Pages          = {184-191},
  abstract       = {Model calculations presented in this article show that
                   commonly used methodology of 15N relaxation data
                   analysis completely fails in detecting nanosecond time
                   scale motions if the major part of the molecule is
                   involved in these motions. New criteria are introduced
                   for the detection of such cases, based on the
                   dependence of the apparent overall correlation time,
                   derived from the T1/T2 ratio, on the spectrometer
                   frequency. Correctly estimating the overall rotation
                   correlation time tauR was shown to play the key role in
                   model-free data analysis. It is found, however, that in
                   cases of slow internal motions with characteristic
                   times of more than 3-4 ns, the effective tauR provided
                   by the T1/T2 ratio for individual amide nitrogens can
                   be used for the characterization of the fast picosecond
                   internal dynamics.},
  authoraddress  = {Shemyakin and Ovchinnikov Institute of Bioorganic
                   Chemistry, Russian Academy of Sciences, Ul.
                   Miklukho-Maklaya 16/10, Moscow, 117871, Russia.},
  keywords       = {Magnetic Resonance Spectroscopy/*methods ; Models,
                   Chemical ; Nitrogen Isotopes ; Proteins/chemistry ;
                   Research Support, Non-U.S. Gov't},
  language       = {eng},
  medline-aid    = {S1090780797911903 [pii]},
  medline-da     = {19971016},
  medline-dcom   = {19971016},
  medline-edat   = {1997/08/01},
  medline-fau    = {Korzhnev, D M ; Orekhov, V Y ; Arseniev, A S},
  medline-is     = {1090-7807},
  medline-jid    = {9707935},
  medline-lr     = {20041117},
  medline-mhda   = {1997/08/01 00:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {9281482},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Nitrogen Isotopes) ; 0 (Proteins)},
  medline-sb     = {IM},
  medline-so     = {J Magn Reson 1997 Aug;127(2):184-91.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=9281482},
  year           = 1997
}

@Article{Korzhnev04a,
  Author         = {Korzhnev, D. M. and Kloiber, K. and Kanelis, V. and
                   Tugarinov, V. and Kay, L. E.},
  Title          = {Probing slow dynamics in high molecular weight
                   proteins by methyl-{TROSY} {NMR} spectroscopy:
                   application to a 723-residue enzyme.},
  Journal        = jacs,
  Volume         = {126},
  Number         = {12},
  Pages          = {3964-3973},
  abstract       = {A new CPMG-based multiple quantum relaxation
                   dispersion experiment is presented for measuring
                   millisecond dynamic processes at side-chain methyl
                   positions in high molecular weight proteins. The
                   experiment benefits from a methyl-TROSY effect in which
                   cancellation of intramethyl dipole fields occurs,
                   leading to methyl (13)C-(1)H correlation spectra of
                   high sensitivity and resolution (Tugarinov, V.; Hwang,
                   P. M.; Ollerenshaw, J. E.; Kay, L. E. J. Am. Chem. Soc.
                   2003, 125, 10420-10428). The utility of the methodology
                   is illustrated with an application to a highly
                   deuterated, methyl-protonated sample of malate synthase
                   G, an 82 kDa enzyme consisting of a single polypeptide
                   chain. A comparison of the sensitivity obtained using
                   the present approach relative to existing HSQC-type
                   (13)C single quantum dispersion experiments shows a
                   gain of a factor of 5.4 on average, significantly
                   increasing the range of applications for this
                   methodology.},
  authoraddress  = {Protein Engineering Network Centres of Excellence and
                   the Departments of Medical Genetics, Biochemistry, and
                   Chemistry, University of Toronto, Toronto, Ontario,
                   Canada M5S 1A8.},
  keywords       = {Carbon Isotopes ; Malate Synthase/*chemistry ; Models,
                   Chemical ; Models, Molecular ; Molecular Weight ;
                   Nuclear Magnetic Resonance, Biomolecular/*methods ;
                   Protein Conformation ; Thermodynamics},
  language       = {eng},
  medline-aid    = {10.1021/ja039587i [doi]},
  medline-crdt   = {2004/03/25 05:00},
  medline-da     = {20040324},
  medline-dcom   = {20040707},
  medline-edat   = {2004/03/25 05:00},
  medline-fau    = {Korzhnev, Dmitry M ; Kloiber, Karin ; Kanelis, Voula ;
                   Tugarinov, Vitali ; Kay, Lewis E},
  medline-is     = {0002-7863 (Print) ; 0002-7863 (Linking)},
  medline-jid    = {7503056},
  medline-jt     = {Journal of the American Chemical Society},
  medline-lr     = {20061115},
  medline-mhda   = {2004/07/09 05:00},
  medline-own    = {NLM},
  medline-pl     = {United States},
  medline-pmid   = {15038751},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article ; Research Support, Non-U.S. Gov't},
  medline-rn     = {0 (Carbon Isotopes) ; EC 2.3.3.9 (Malate Synthase)},
  medline-sb     = {IM},
  medline-so     = {J Am Chem Soc. 2004 Mar 31;126(12):3964-73.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=15038751},
  doi            = {10.1021/ja039587i},
  year           = 2004
}

@Article{Korzhnev04b,
  Author         = {Korzhnev, D. M. and Kloiber, K. and Kay, L. E.},
  Title          = {Multiple-quantum relaxation dispersion {NMR}
                   spectroscopy probing millisecond time-scale dynamics in
                   proteins: theory and application.},
  Journal        = jacs,
  Volume         = {126},
  Number         = {23},
  Pages          = {7320-7329},
  abstract       = {New relaxation dispersion experiments are presented
                   that probe millisecond time-scale dynamical processes
                   in proteins. The experiments measure the relaxation of
                   (1)H-(15)N multiple-quantum coherence as a function of
                   the rate of application of either (1)H or (15)N
                   refocusing pulses during a constant time relaxation
                   interval. In contrast to the dispersion profiles
                   generated from more conventional (15)N((1)H)
                   single-quantum relaxation experiments that depend on
                   changes in (15)N((1)H) chemical shifts between
                   exchanging states, (1)H-(15)N multiple-quantum
                   dispersions are sensitive to changes in the chemical
                   environments of both (1)H and (15)N spins. The
                   resulting multiple-quantum relaxation dispersion
                   profiles can, therefore, be quite different from those
                   generated by single-quantum experiments, so that an
                   analysis of both single- and multiple-quantum profiles
                   together provides a powerful approach for obtaining
                   robust measures of exchange parameters. This is
                   particularly the case in applications to protonated
                   proteins where other methods for studying exchange
                   involving amide proton spins are negatively influenced
                   by contributions from neighboring protons. The
                   methodology is demonstrated on protonated and
                   perdeuterated samples of a G48M mutant of the Fyn SH3
                   domain that exchanges between folded and unfolded
                   states in solution.},
  authoraddress  = {Protein Engineering Network Centres of Excellence and
                   the Department of Medical Genetics, University of
                   Toronto, Toronto, Ontario, Canada M5S 1A8.},
  keywords       = {*Magnetic Resonance Spectroscopy ; Protein Folding ;
                   Proto-Oncogene Proteins/*chemistry/*metabolism ;
                   Proto-Oncogene Proteins c-fyn ; Time Factors ; src
                   Homology Domains},
  language       = {eng},
  medline-aid    = {10.1021/ja049968b [doi]},
  medline-crdt   = {2004/06/10 05:00},
  medline-da     = {20040609},
  medline-dcom   = {20040923},
  medline-edat   = {2004/06/10 05:00},
  medline-fau    = {Korzhnev, Dmitry M ; Kloiber, Karin ; Kay, Lewis E},
  medline-is     = {0002-7863 (Print) ; 0002-7863 (Linking)},
  medline-jid    = {7503056},
  medline-jt     = {Journal of the American Chemical Society},
  medline-lr     = {20091119},
  medline-mhda   = {2004/09/24 05:00},
  medline-own    = {NLM},
  medline-pl     = {United States},
  medline-pmid   = {15186169},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article ; Research Support, Non-U.S. Gov't},
  medline-rn     = {0 (Proto-Oncogene Proteins) ; EC 2.7.10.2
                   (Proto-Oncogene Proteins c-fyn)},
  medline-sb     = {IM},
  medline-so     = {J Am Chem Soc. 2004 Jun 16;126(23):7320-9.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=15186169},
  doi            = {10.1021/ja049968b},
  year           = 2004
}

@Article{Korzhnev05a,
  Author         = {Korzhnev, D. M. and Orekhov, V. Y. and Kay, L. E.},
  Title          = {Off-resonance {R}(1rho) {NMR} studies of exchange
                   dynamics in proteins with low spin-lock fields: an
                   application to a {F}yn {SH}3 domain.},
  Journal        = jacs,
  Volume         = {127},
  Number         = {2},
  Pages          = {713-721},
  abstract       = {An (15)N NMR R(1rho) relaxation experiment is
                   presented for the measurement of millisecond time scale
                   exchange processes in proteins. On- and off-resonance
                   R(1rho) relaxation profiles are recorded one residue at
                   a time using a series of one-dimensional experiments in
                   concert with selective Hartmann-Hahn polarization
                   transfers. The experiment can be performed using low
                   spin-lock field strengths (values as low as 25 Hz have
                   been tested), with excellent alignment of magnetization
                   along the effective field achieved. Additionally,
                   suppression of the effects of cross-correlated
                   relaxation between dipolar and chemical shift
                   anisotropy interactions and (1)H-(15)N scalar coupled
                   evolution is straightforward to implement, independent
                   of the strength of the (15)N spin-locking field. The
                   methodology is applied to study the folding of a G48M
                   mutant of the Fyn SH3 domain that has been
                   characterized previously by CPMG dispersion
                   experiments. It is demonstrated through experiment that
                   off-resonance R(1rho) data measured at a single
                   magnetic field and one or more spin-lock field
                   strengths, with amplitudes on the order of the rate of
                   exchange, allow a complete characterization of a
                   two-site exchange process. This is possible even in the
                   case of slow exchange on the NMR time scale, where
                   complementary approaches involving CPMG-based
                   experiments fail. Advantages of this methodology in
                   relation to other approaches are described.},
  authoraddress  = {Protein Engineering Network Centers of Excellence and
                   Department of Medical Genetics, The University of
                   Toronto, Toronto, Ontario, Canada M5S 1A8.},
  keywords       = {Nitrogen Isotopes ; Nuclear Magnetic Resonance,
                   Biomolecular/*methods ; Protein Folding ;
                   Proto-Oncogene Proteins/*chemistry ; Proto-Oncogene
                   Proteins c-fyn ; src Homology Domains ; src-Family
                   Kinases/*chemistry},
  language       = {eng},
  medline-aid    = {10.1021/ja0446855 [doi]},
  medline-crdt   = {2005/01/13 09:00},
  medline-da     = {20050112},
  medline-dcom   = {20050303},
  medline-edat   = {2005/01/13 09:00},
  medline-fau    = {Korzhnev, Dmitry M ; Orekhov, Vladislav Yu ; Kay,
                   Lewis E},
  medline-is     = {0002-7863 (Print) ; 0002-7863 (Linking)},
  medline-jid    = {7503056},
  medline-jt     = {Journal of the American Chemical Society},
  medline-lr     = {20091119},
  medline-mhda   = {2005/03/04 09:00},
  medline-own    = {NLM},
  medline-pl     = {United States},
  medline-pmid   = {15643897},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article ; Research Support, Non-U.S. Gov't},
  medline-rn     = {0 (Nitrogen Isotopes) ; 0 (Proto-Oncogene Proteins) ;
                   EC 2.7.10.2 (Proto-Oncogene Proteins c-fyn) ; EC
                   2.7.10.2 (src-Family Kinases)},
  medline-sb     = {IM},
  medline-so     = {J Am Chem Soc. 2005 Jan 19;127(2):713-21.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=15643897},
  doi            = {10.1021/ja0446855},
  year           = 2005
}

@Article{Korzhnev05b,
  Author         = {Korzhnev, D. M. and Neudecker, P. and Mittermaier, A.
                   and Orekhov, V. Y. and Kay, L. E.},
  Title          = {Multiple-site exchange in proteins studied with a
                   suite of six {NMR} relaxation dispersion experiments:
                   an application to the folding of a {F}yn {SH}3 domain
                   mutant.},
  Journal        = jacs,
  Volume         = {127},
  Number         = {44},
  Pages          = {15602-15611},
  abstract       = {The three-site exchange folding reaction of an
                   (15)N-labeled, highly deuterated Gly48Met mutant of the
                   Fyn SH3 domain has been characterized at 25 degrees C
                   using a suite of six CPMG-type relaxation dispersion
                   experiments that measure exchange contributions to
                   backbone (1)H and (15)N transverse relaxation rates in
                   proteins. It is shown that this suite of experiments
                   allows the extraction of all the parameters of this
                   multisite exchange process in a robust manner,
                   including chemical shift differences between exchanging
                   states, from a data set recorded at only a single
                   temperature. The populations of the exchanging folded,
                   intermediate, and unfolded states that are fit are 94,
                   0.7, and 5\%, respectively. Despite the small fraction
                   of the intermediate, structural information is obtained
                   for this state that is consistent with the picture of
                   SH3 domain folding that has emerged from other studies.
                   Taken together, the six dispersion experiments
                   facilitate the complete reconstruction of (1)H-(15)N
                   correlation spectra for the unfolded and intermediate
                   states that are "invisible" in even the most sensitive
                   of NMR experiments.},
  authoraddress  = {Departments of Medical Genetics, Biochemistry, and
                   Chemistry, The University of Toronto, Toronto, Ontario
                   M5S 1A8, Canada.},
  keywords       = {Deuterium Exchange Measurement ; Magnetic Resonance
                   Spectroscopy/*methods ; Mutation ; Nitrogen Isotopes ;
                   *Protein Folding ; Proteins/*chemistry ; Proto-Oncogene
                   Proteins c-fyn/*chemistry/genetics ; src Homology
                   Domains},
  language       = {eng},
  medline-aid    = {10.1021/ja054550e [doi]},
  medline-crdt   = {2005/11/03 09:00},
  medline-da     = {20051102},
  medline-dcom   = {20060208},
  medline-edat   = {2005/11/03 09:00},
  medline-fau    = {Korzhnev, Dmitry M ; Neudecker, Philipp ; Mittermaier,
                   Anthony ; Orekhov, Vladislav Yu ; Kay, Lewis E},
  medline-is     = {0002-7863 (Print) ; 0002-7863 (Linking)},
  medline-jid    = {7503056},
  medline-jt     = {Journal of the American Chemical Society},
  medline-lr     = {20120605},
  medline-mhda   = {2006/02/09 09:00},
  medline-own    = {NLM},
  medline-pl     = {United States},
  medline-pmid   = {16262426},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article ; Research Support, Non-U.S. Gov't},
  medline-rn     = {0 (Nitrogen Isotopes) ; 0 (Proteins) ; EC 2.7.10.2
                   (FYN protein, human) ; EC 2.7.10.2 (Proto-Oncogene
                   Proteins c-fyn)},
  medline-sb     = {IM},
  medline-so     = {J Am Chem Soc. 2005 Nov 9;127(44):15602-11.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=16262426},
  doi            = {10.1021/ja054550e},
  year           = 2005
}

@Article{KullbackLeibler51,
  Author         = {Kullback, S. and Leibler, R. A.},
  Title          = {On information and sufficiency},
  Journal        = ams,
  Volume         = {22},
  Number         = {1},
  Pages          = {79-86},
  address        = {IMS Business Office-Suite 7, 3401 Investment Blvd,
                   Hayward, CA 94545},
  citedref       = {BHATTACHARYYA A, 1943, B CALCUTTA MATH SOC, V35, P99 ;
                   BHATTACHARYYA A, 1946, SANKHYA, V7, P401 ; BROWN GW,
                   1950, J CLIN PSYCHOL, V6, P58 ; DOOB JL, 1936, T AM
                   MATH SOC, V39, P410 ; DOOB JS, 1934, T AM MATH SOC,
                   V36, P759 ; FISHER RA, 1921, PHILOS T ROY SOC A, V222,
                   P309 ; FISHER RA, 1925, P CAMB PHILOS SOC, V22, P700 ;
                   HALMOS PR, 1949, ANN MATH STAT, V20, P225 ; HALMOS PR,
                   1950, MEASURE THEORY ; HARDY GH, 1934, INEQUALITIES ;
                   JEFFREYS H, 1946, P ROY SOC LOND A MAT, V186, P453 ;
                   JEFFREYS H, 1948, THEORY PROBABILITY ; KOLMOGOROFF A,
                   1933, ERGEBNISSE MATH IHRE ; LEHMANN EL, 1950, ANN MATH
                   STAT, V21, P1 ; MAHALANOBIS PC, 1936, P NAT I SCI
                   INDIA, V2 ; MOURIER E, 1946, COMPT REND ACAD SCI, V223,
                   P712 ; SHANNON CE, 1948, BELL SYST TECH J, V27, P379 ;
                   SHANNON CE, 1948, BELL SYST TECH J, V27, P623 ; SHANNON
                   CE, 1949, MATH THEORY COMMUNIC ; WELCH BL, 1939,
                   BIOMETRIKA, V31, P218 ; WIENER N, 1948, CYBERNETICS},
  isifile-dt     = {Article},
  isifile-ga     = {UM018},
  isifile-j9     = {Ann Math Statist},
  isifile-nr     = {21},
  isifile-pi     = {Hayward},
  isifile-sc     = {Mathematics},
  isifile-tc     = {807},
  issn           = {0003-4851},
  language       = {English},
  publisher      = {Inst Mathematical Statistics},
  size           = {8 p.},
  sourceid       = {ISI:A1951UM01800005},
  doi            = {10.1214/aoms/1177729694},
  year           = 1951
}

@Article{Larsson03,
  Author         = {Larsson, G. and Martinez, G. and Schleucher, J. and
                   Wijmenga, S. S.},
  Title          = {Detection of nano-second internal motion and
                   determination of overall tumbling times independent of
                   the time scale of internal motion in proteins from
                   {NMR} relaxation data.},
  Journal        = jbnmr,
  Volume         = {27},
  Number         = {4},
  Pages          = {291-312},
  abstract       = {The usual analysis of (15)N relaxation data of
                   proteins is straightforward as long as the assumption
                   can be made that the backbone of most residues only
                   undergoes fast (ps), small amplitude internal motions.
                   If this assumption cannot be made, as for example for
                   proteins which undergo domain motions or for unfolded
                   or partially folded proteins, one needs a method to
                   establish for each residue whether it undergoes fast
                   (ps) or slow (ns) internal motion. Even then it is
                   impossible to determine the correct overall tumbling
                   time, tau(m)(0), via the usual method from the ratio of
                   the longitudinal and transverse relaxation times, if
                   the majority of residues do not undergo fast, small
                   amplitude internal motions. The latter problem is
                   solved when tau(m)(0) can be determined independent of
                   the time scale, tau(i), or the amplitude, S(2), of the
                   internal motion. We propose a new protocol, called
                   PINATA, for analyzing (15)N relaxation data acquired at
                   minimally two field strengths, where no a priori
                   assumption about time scales or amplitude of internal
                   motions needs to be made, and overall tumbling can
                   either be isotropic or anisotropic. The protocol
                   involves four steps. First, for each residue, it is
                   detected whether it undergoes ps- or ns-internal
                   motion, via the combination of the ratio of the
                   longitudinal relaxation time at two fields and the
                   hetero-nuclear NOE. Second, for each residue tau(m)(0)
                   and the exchange broadening, Rex, are iteratively
                   determined. The accuracy of the determination of
                   tau(m)(0) is ca. +/-0.5 ns and of Rex ca +/- 0.7 s(-1),
                   when the relaxation data are of good quality and
                   tau(m)(0)>5 ns, S(2)>0.3, and tau(i)< approximately 3
                   ns. Third, given tau(m)(0) and Rex, step 1 is repeated
                   to iteratively improve on the internal motion and
                   obtain better estimates of the internal parameter
                   values. Fourth, final time scales and amplitudes for
                   internal motions are determined via grid search based
                   fitting and chi(2)-analysis. The protocol was
                   successfully tested on synthetic and experimental data
                   sets. The synthetic dataset mimics internal motions on
                   either fast or slow time scales, or a combination of
                   both, of either small- or large amplitude, superimposed
                   onto anisotropic overall motion. The procedures are
                   incorporated into MATLAB scripts, which are available
                   on request.},
  authoraddress  = {Department of Medical Biochemistry and Biophysics Umea
                   University, SE-901 87 Umea, Sweden.},
  keywords       = {Algorithms ; Kinetics ; Magnetics ; Models,
                   Theoretical ; Motion ; Nitrogen Isotopes ; Nuclear
                   Magnetic Resonance, Biomolecular/*methods ;
                   Proteins/*chemistry ; Research Support, Non-U.S. Gov't},
  language       = {eng},
  medline-aid    = {5143024 [pii]},
  medline-da     = {20030926},
  medline-dcom   = {20040709},
  medline-edat   = {2003/09/27 05:00},
  medline-fau    = {Larsson, Goran ; Martinez, Gary ; Schleucher, Jurgen ;
                   Wijmenga, Sybren S},
  medline-is     = {0925-2738},
  medline-jid    = {9110829},
  medline-lr     = {20041117},
  medline-mhda   = {2004/07/10 05:00},
  medline-own    = {NLM},
  medline-pl     = {Netherlands},
  medline-pmid   = {14512728},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Nitrogen Isotopes) ; 0 (Proteins)},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR 2003 Dec;27(4):291-312.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=14512728},
  year           = 2003
}

@Article{Lee97,
  Author         = {Lee, L. K. and Rance, M. and Chazin, W. J. and Palmer,
                   A. G.},
  Title          = {Rotational diffusion anisotropy of proteins from
                   simultaneous analysis of {N}-15 and {C}-13(alpha)
                   nuclear spin relaxation},
  Journal        = jbnmr,
  Volume         = {9},
  Number         = {3},
  Pages          = {287-298},
  abstract       = {Current methods of determining the rotational
                   diffusion tensors of proteins in solution by NMR
                   spectroscopy exclusively utilize relaxation rate
                   constants for backbone amide N-15 spins. However, the
                   distributions of orientations of N-H bond vectors are
                   not isotropic in many proteins, and correlations
                   between bond vector orientations reduce the accuracy
                   and precision of rotational diffusion tensors extracted
                   from N-15 spin relaxation data. The inclusion of both
                   C-13(alpha) and N-15 Spin relaxation rate constants
                   increases the robustness of the diffusion tensor
                   analysis because the orientations of the
                   C-alpha-H-alpha bond vectors differ from the
                   orientations of the N-H bond vectors. Theoretical and
                   experimental results for calbindin D-9k, granulocyte
                   colony stimulating factor, and ubiquitin, three
                   proteins with different distributions of N-H and
                   C-alpha-H-alpha bond vectors, are used to illustrate
                   the advantages of the simultaneous utilization of
                   C-13(alpha) and N-15 relaxation data.},
  address        = {Spuiboulevard 50, PO Box 17, 3300 AA Dordrecht,
                   Netherlands},
  authoraddress  = {Columbia Univ, Dept Biochem \& Mol Biophys, New York,
                   NY 10032 USA. ; Univ Cincinnati, Dept Mol Genet Biochem
                   \& Mol Biol, Cincinnati, OH 45267 USA. ; Scripps Res
                   Inst, Dept Mol Biol, LA Jolla, CA 92037 USA.},
  citedref       = {ABRAGAM A, 1961, PRINCIPLES NUCLEAR M ; BARBATO G,
                   1992, BIOCHEMISTRY-US, V31, P5269 ; BRINK DM, 1993,
                   ANGULAR MOMENTUM ; BRUSCHWEILER R, 1995, SCIENCE, V268,
                   P886 ; CLORE GM, 1990, BIOCHEMISTRY-US, V29, P7387 ;
                   DEVORE J, 1982, PROBABILITY STAT ENG ; FARROW NA, 1994,
                   BIOCHEMISTRY-US, V33, P5984 ; FARROW NA, 1995, J BIOMOL
                   NMR, V6, P153 ; HILL CP, 1993, P NATL ACAD SCI USA,
                   V90, P5167 ; ISHIMA R, 1995, J MAGN RESON SER B, V108,
                   P73 ; KAY LE, 1989, BIOCHEMISTRY-US, V28, P8972 ;
                   KORDEL J, 1992, BIOCHEMISTRY-US, V31, P4856 ; KORDEL J,
                   1993, J MOL BIOL, V231, P711 ; LIPARI G, 1982, J AM
                   CHEM SOC, V104, P4546 ; LIPARI G, 1982, J AM CHEM SOC,
                   V104, P4559 ; MACKAY JP, 1996, BIOCHEMISTRY-US, V35,
                   P4867 ; MANDEL AM, 1995, J MOL BIOL, V246, P144 ;
                   MANDEL AM, 1996, BIOCHEMISTRY-US, V35, P16009 ;
                   MOSTELLER F, 1977, DATA ANAL REGRESSION ; PALMER AG,
                   1996, J PHYS CHEM-US, V100, P13293 ; PENG JW, 1992, J
                   MAGN RESON, V98, P308 ; PRESS WH, 1992, NUMERICAL
                   RECIPES AR ; SCHURR JM, 1994, J MAGN RESON SER B, V105,
                   P211 ; SKELTON NJ, 1993, J MAGN RESON SER B, V102, P253
                   ; SVENSSON LA, 1992, J MOL BIOL, V223, P601 ; TJANDRA
                   N, 1995, J AM CHEM SOC, V117, P12562 ; VIJAYKUMAR S,
                   1987, J MOL BIOL, V194, P531 ; VISWANATH DS, 1989, DATA
                   BOOK VISCOSITY ; WOESSNER DE, 1962, J CHEM PHYS, V37,
                   P647 ; ZHENG Z, 1995, BIOCHEMISTRY-US, V34, P5212 ;
                   ZINK T, 1994, BIOCHEMISTRY-US, V33, P8453},
  isifile-dt     = {Article},
  isifile-ga     = {XF937},
  isifile-j9     = {J Biomol NMR},
  isifile-ji     = {J. Biomol. NMR},
  isifile-nr     = {31},
  isifile-pi     = {Dordrecht},
  isifile-sc     = {Biochemistry \& Molecular Biology; Spectroscopy},
  isifile-tc     = {177},
  issn           = {0925-2738},
  keywords       = {proteins; nuclear spin relaxation; rotational
                   diffusion tensor anisotropy ; [ISI:] calcium-loaded
                   calbindin-d(9k); magnetic-resonance relaxation;
                   colony-stimulating factor; model-free approach;
                   backbone dynamics; nmr-spectroscopy; macromolecules;
                   resolution; range ;;},
  language       = {English},
  month          = {Apr},
  publisher      = {Kluwer Academic Publ},
  size           = {12 p.},
  sourceid       = {ISI:A1997XF93700006},
  doi            = {10.1023/a:1018631009583},
  year           = 1997
}

@Article{Lefevre96,
  Author         = {Lefevre, J.F. and Dayie, K.T. and Peng, J.W. and
                   Wagner, G.},
  Title          = {Internal mobility in the partially folded {DNA}
                   binding and dimerization domains of {GAL}4: {NMR}
                   analysis of the {N}-{H} spectral density functions.},
  Journal        = biochem,
  Volume         = {35},
  Number         = {8},
  Pages          = {2674-2686},
  abstract       = {The DNA binding domain (residues 1--65) of the yeast
                   transcriptional activator GAL4 is only partially
                   folded. While residues 10-41, the DNA recognition
                   domain, form a well-defined structure in the free
                   protein, the whole polypeptide folds up and dimerizes
                   upon binding DNA. In order to describe the mobility of
                   the protein, we have characterized the frequency
                   spectrum of the motions of N-H bond vectors of
                   GAL4(1-65) using a reduced spectral density mapping
                   approach (an approximation of the full spectral density
                   mapping technique) [Peng, J. W., & Wagner, G. (1992a)
                   J. Magn. Reson. 98, 308-332; Peng. J. W., & Wagner, G.
                   (1992b) Biochemistry 31, 8571-8586]. 15N spin-lattice
                   relaxation [Rn(Nz)], spin-spin relaxation [Rn(Nx,y)],
                   cross-relaxation [RN(Hz-->Nz)], two-spin order
                   [RNH(2HzNz)], and antiphase [RNH(2HzNx,y)] rates were
                   determined for 52 of the 65 backbone amide groups at 10
                   degrees C and ph 6.5 at 11.74 T. Calculations of the
                   spectral density functions using a reduced set of
                   RN(Nz),RN(Nx,y),RN(Hz-->Nz), and RNH(2HzNz) gave
                   excellent agreement with those calculated using all six
                   sets. The reduced method has the added advantage that
                   the errant behavior seen at high field values is
                   circumvented. A linear correlation was found between
                   J(omega N) and J(0) with a limited and clearly defined
                   range of J(0) values which defines the range of rates
                   for internal motions in GAL4(1-65). It appears that all
                   residues experience a combination of two movements: one
                   of the overall tumbling (correlation time, 8.65 ns) and
                   the other of fast internal fluctuations of the
                   structure. The respective weights of these
                   contributions vary with the primary sequence and
                   faithfully mirror the secondary and tertiary elements
                   of the protein. The position on the correlation line of
                   J(omega N) versus J(0) indicates the amount of angular
                   averaging relative to the overall motion of the
                   protein. A spectral density function for internal
                   motions can be described.},
  authoraddress  = {Department of Biological Chemistry and Molecular
                   Pharmacology, Harvard Medical School, Boston,
                   Massachusetts 02115, USA.},
  keywords       = {Amino Acid Sequence ; Binding Sites ; DNA,
                   Fungal/metabolism ; DNA-Binding
                   Proteins/*chemistry/genetics/metabolism ; Fungal
                   Proteins/*chemistry/genetics/metabolism ; Magnetic
                   Resonance Spectroscopy ; Models, Molecular ; Molecular
                   Sequence Data ; Molecular Structure ; Protein
                   Conformation ; Protein Folding ; Research Support,
                   Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S. ;
                   Saccharomyces cerevisiae/chemistry/genetics/metabolism
                   ; *Saccharomyces cerevisiae Proteins ;
                   Trans-Activators/*chemistry/genetics/metabolism ;
                   *Transcription Factors},
  language       = {eng},
  doi            = {10.1021/bi9526802},
  medline-aid    = {10.1021/bi9526802 [doi] ; bi9526802 [pii]},
  medline-da     = {19960605},
  medline-dcom   = {19960605},
  medline-edat   = {1996/02/27},
  medline-fau    = {Lefevre, J F ; Dayie, K T ; Peng, J W ; Wagner, G},
  medline-gr     = {GM47467/GM/NIGMS},
  medline-is     = {0006-2960 (Print)},
  medline-jid    = {0370623},
  medline-jt     = {Biochemistry.},
  medline-lr     = {20041117},
  medline-mhda   = {1996/02/27 00:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {8611573},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (DNA, Fungal) ; 0 (DNA-Binding Proteins) ; 0 (Fungal
                   Proteins) ; 0 (GAL4 protein, S cerevisiae) ; 0
                   (Saccharomyces cerevisiae Proteins) ; 0
                   (Trans-Activators) ; 0 (Transcription Factors)},
  medline-sb     = {IM},
  medline-so     = {Biochemistry. 1996 Feb 27;35(8):2674-86.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=8611573},
  year           = 1996
}

@Article{Levenberg44,
  Author         = {Levenberg, K.},
  Title          = {A method for the solution of certain non-linear
                   problems in least squares},
  Journal        = qam,
  Volume         = {2},
  Pages          = {164-168},
  year           = 1944
}

@Book{LinhartZucchini86,
  Author         = {H Linhart and W Zucchini},
  Title          = {Model Selection},
  Publisher      = {John Wiley \& Sons, Inc.},
  Series         = {Wiley Series in Probability and Mathematical
                   Statistics},
  Address        = {New York, NY, USA},
  isbn           = {0-471-83722-9},
  year           = 1986
}

@Article{LipariSzabo82a,
  Author         = {Lipari, G. and Szabo, A.},
  Title          = {Model-free approach to the interpretation of nuclear
                   magnetic-resonance relaxation in macromolecules {I}.
                   {T}heory and range of validity},
  Journal        = jacs,
  Volume         = {104},
  Number         = {17},
  Pages          = {4546-4559},
  address        = {1155 16TH ST, NW, Washington, DC 20036},
  authoraddress  = {NIADDKD,Chem Phys Lab,Bethesda,MD 20205.},
  citedref       = {BOCIAN DF, 1978, ANNU REV PHYS CHEM, V29, P307 ;
                   BRAINARD JR, 1981, BIOCHEMISTRY-US, V20, P4618 ; BRINK
                   DM, 1968, ANGULAR MOMENTUM ; BULL TE, 1978, J AM CHEM
                   SOC, V100, P4643 ; DILL K, 1979, J AM CHEM SOC, V101,
                   P4376 ; HOWARTH OW, 1979, J CHEM SOC FARAD T 2, V75,
                   P863 ; KING R, 1978, BIOPHYS J, V6, P103 ; KING R,
                   1978, CHEM PHYS LETT, V55, P15 ; KINOSITA K, 1977,
                   BIOPHYS J, V20, P289 ; LEVY RM, 1981, J AM CHEM SOC,
                   V103, P5998 ; LEVY RM, 1981, J AM CHEM SOC, V103, P994
                   ; LIPARI G, 1980, BIOPHYS J, V30, P489 ; LIPARI G,
                   1981, BIOCHEMISTRY-US, V20, P6250 ; LIPARI G, 1981, J
                   CHEM PHYS, V75, P2971 ; LONDON RE, 1978, J AM CHEM SOC,
                   V100, P7159 ; LONDON RE, 1980, MAGNETIC RESONANCE B,
                   V1, P1 ; RIBEIRO AA, 1980, J AM CHEM SOC, V102, P4040 ;
                   RICHARZ R, 1980, BIOCHEMISTRY-US, V19, P5189 ; SCHAEFER
                   J, 1973, MACROMOLECULES, V6, P882 ; SZABO A, 1980, J
                   CHEM PHYS, V72, P4620 ; WALLACH D, 1967, J CHEM PHYS,
                   V47, P5258 ; WITTEBORT RJ, 1978, J CHEM PHYS, V69,
                   P1722 ; WITTEBORT RJ, 1980, J AM CHEM SOC, V102, P5723
                   ; WOESSNER DE, 1962, J CHEM PHYS, V36, P1},
  isifile-dt     = {Article},
  isifile-ga     = {PC829},
  isifile-j9     = {J Amer Chem Soc},
  isifile-ji     = {J. Am. Chem. Soc.},
  isifile-nr     = {24},
  isifile-pi     = {Washington},
  isifile-sc     = {Chemistry, Multidisciplinary},
  isifile-tc     = {1642},
  issn           = {0002-7863},
  language       = {English},
  publisher      = {Amer Chemical Soc},
  size           = {14 p.},
  sourceid       = {ISI:A1982PC82900009},
  year           = 1982,
  doi            = {10.1021/ja00381a009}
}

@Article{LipariSzabo82b,
  Author         = {Lipari, G. and Szabo, A.},
  Title          = {Model-free approach to the interpretation of nuclear
                   magnetic-resonance relaxation in macromolecules {II}.
                   {A}nalysis of experimental results},
  Journal        = jacs,
  Volume         = {104},
  Number         = {17},
  Pages          = {4559-4570},
  abstract       = {For pt.I see ibid., vol.104, p.4546 (1982). In the
                   preceding paper it has been shown that the unique
                   dynamic information on fast internal motions in an NMR
                   relaxation experiment on macromolecules in solution is
                   specified by a generalized order parameter, S , and an
                   effective correlation time, tau /sub e/. The authors
                   now deal with the extraction and interpretation of this
                   information. The procedure used to obtain S /sup 2/ and
                   tau /sub e/ from experimental data by using a
                   least-squares method and, in certain favorable
                   circumstances, by using an analytical formula is
                   described. A variety of experiments are then analyzed
                   to yield information on the time scale and spatial
                   restriction of internal motions of isoleucines in
                   myoglobin, methionines in dihydrofolate reductase and
                   myoglobin, a number of aliphatic residues in basic
                   pancreatic trypsin inhibitor, and ethyl isocyanide
                   bound to myoglobin, hemoglobin, and aliphatic side
                   chains in three random-coil polymers. The numerical
                   values of S /sup 2/ and tau /sub e / can be readily
                   interpreted within the framework of a variety of
                   models.},
  address        = {1155 16TH ST, NW, Washington, DC 20036},
  authoraddress  = {NIADDKD,Chem Phys Lab,Bethesda,MD 20205.},
  citedref       = {BLAKLEY RL, 1978, BIOCHEMISTRY-US, V17, P2284 ;
                   BRAINARD JR, 1981, BIOCHEMISTRY-US, V20, P4618 ; FREY
                   MN, 1973, ACTA CRYSTALLOGR B, V29, P876 ; GHESQUIERE D,
                   1979, MACROMOLECULES, V12, P775 ; GILMAN JG, 1979,
                   BIOCHEMISTRY-US, V18, P2273 ; HOWARTH OW, 1979, J CHEM
                   SOC FARAD T 2, V75, P863 ; JONES WC, 1976, J BIOL CHEM,
                   V251, P7452 ; KARPLUS M, 1979, NATURE, V277, P578 ;
                   KINOSITA K, 1977, BIOPHYS J, V20, P289 ; LEHMANN MS,
                   1972, J AM CHEM SOC, V94, P2657 ; LEVY GC, 1978, J AM
                   CHEM SOC, V100, P410 ; LEVY RM, 1981, J AM CHEM SOC,
                   V103, P5998 ; LIPARI G, 1980, BIOPHYS J, V30, P489 ;
                   LIPARI G, 1981, J CHEM PHYS, V75, P2971 ; LIPARI G,
                   1982, J AM CHEM SOC, V104, P4546 ; LONDON RE, 1978, J
                   AM CHEM SOC, V100, P7159 ; MCCAMMON JA, 1977, NATURE,
                   V267, P585 ; RIBEIRO AA, 1980, J AM CHEM SOC, V102,
                   P4040 ; RICHARZ R, 1980, BIOCHEMISTRY-US, V19, P5189 ;
                   WALLACH D, 1967, J CHEM PHYS, V47, P5258 ; WANG CC,
                   1980, J CHEM PHYS, V72, P5333 ; WERBELOW LG, 1977, ADV
                   MAGN RESON, V9, P189 ; WITTEBORT RJ, 1978, J CHEM PHYS,
                   V69, P1722 ; WITTEBORT RJ, 1979, P NATL ACAD SCI USA,
                   V76, P1059 ; WITTEBORT RJ, 1980, J AM CHEM SOC, V102,
                   P5723 ; WOESSNER DE, 1962, J CHEM PHYS, V36, P1},
  isifile-dt     = {Article},
  isifile-ga     = {PC829},
  isifile-j9     = {J Amer Chem Soc},
  isifile-ji     = {J. Am. Chem. Soc.},
  isifile-nr     = {26},
  isifile-pi     = {Washington},
  isifile-sc     = {Chemistry, Multidisciplinary},
  isifile-tc     = {839},
  issn           = {0002-7863},
  language       = {English},
  publisher      = {Amer Chemical Soc},
  size           = {12 p.},
  sourceid       = {ISI:A1982PC82900010},
  year           = 1982,
  doi            = {10.1021/ja00381a010}
}

@Article{Luginbuhl97,
  Author         = {Luginb{\"u}hl, P. and Pervushin, K. V. and Iwai, H.
                   and W{\"u}thrich, K.},
  Title          = {Anisotropic molecular rotational diffusion in 15{N}
                   spin relaxation studies of protein mobility.},
  Journal        = biochem,
  Volume         = {36},
  Number         = {24},
  Pages          = {7305-7312},
  abstract       = {The backbone dynamics of the uniformly 15N-labeled
                   N-terminal 63-residue DNA-binding domain of the 434
                   repressor has been characterized by measurements of the
                   individual 15N longitudinal relaxation times, T1,
                   transverse relaxation times, T2, and heteronuclear
                   15N[1H]-NOEs at 1H resonance frequencies of 400 and 750
                   MHz. The dependence of an apparent spherical top
                   correlation time, tauR, on the orientation of the N-H
                   bond vector with respect to the principal axes of the
                   global diffusion tensor of the protein was used to
                   establish the fact that the degree of anisotropy of the
                   global molecular tumbling amounts to 1.2, which is in
                   good agreement with the values obtained from model
                   calculations of the hydrodynamic properties. A
                   model-free analysis showed that even this small
                   anisotropy leads to the implication of artifactual slow
                   internal motions for at least two residues when the
                   assumption of isotropic global motion is used.
                   Additional residues may actually undergo internal
                   motions on the same time scale as the global rotational
                   diffusion, in which case the model-free approach would,
                   however, be inappropriate for quantifying the
                   correlation times and order parameters. Overall, the
                   experiments with 434(1-63) demonstrate that the
                   assumption of isotropic rotational reorientation may
                   result in artifacts of model-free interpretations of
                   spin relaxation data even for proteins with small
                   deviations from spherical shape.},
  authoraddress  = {Institut fur Molekularbiologie und Biophysik,
                   Eidgenossische Technische Hochschule-Honggerberg,
                   Zurich, Switzerland.},
  keywords       = {Binding Sites ; Chemistry, Physical ; DNA/metabolism ;
                   Escherichia coli ; Hydrogen-Ion Concentration ;
                   Magnetic Resonance Spectroscopy ; Models, Molecular ;
                   Molecular Structure ; Protein Conformation ;
                   Recombinant Proteins ; Repressor
                   Proteins/*chemistry/metabolism ; Research Support,
                   Non-U.S. Gov't ; Solutions},
  language       = {eng},
  doi            = {10.1021/bi963161h},
  medline-aid    = {10.1021/bi963161h [doi] ; bi963161h [pii]},
  medline-da     = {19970710},
  medline-dcom   = {19970710},
  medline-edat   = {1997/06/17},
  medline-fau    = {Luginbuhl, P ; Pervushin, K V ; Iwai, H ; Wuthrich, K},
  medline-is     = {0006-2960},
  medline-jid    = {0370623},
  medline-lr     = {20041117},
  medline-mhda   = {1997/06/17 00:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {9200679},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Recombinant Proteins) ; 0 (Repressor Proteins) ; 0
                   (Solutions) ; 0 (repressor protein 434) ; 9007-49-2
                   (DNA)},
  medline-sb     = {IM},
  medline-so     = {Biochemistry 1997 Jun 17;36(24):7305-12.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=9200679},
  year           = 1997
}

@Article{LuzMeiboom63,
  Author         = {Luz, Z. and Meiboom, S.},
  Title          = {Nuclear magnetic resonance study of protolysis of
                   trimethylammonium ion in aqueous solution - order of
                   reaction with respect to solvent},
  Journal        = jcp,
  Volume         = {39},
  Number         = {2},
  Pages          = {366-370},
  address        = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD,
                   WOODBURY, NY 11797-2999},
  doc-delivery-number = {4164B},
  doi            = {10.1063/1.1734254},
  issn           = {0021-9606},
  journal-iso    = {J. Chem. Phys.},
  language       = {English},
  number-of-cited-references = {13},
  publisher      = {AMER INST PHYSICS},
  research-areas = {Physics},
  times-cited    = {375},
  type           = {Article},
  unique-id      = {ISI:A19634164B00022},
  web-of-science-categories = {Physics, Atomic, Molecular \& Chemical},
  year           = 1963
}

@Article{Mackay96,
  Author         = {MacKay, J. P. and Shaw, G. L. and King, G. F.},
  Title          = {Backbone dynamics of the c-{J}un leucine zipper: 15{N}
                   {NMR} relaxation studies.},
  Journal        = biochem,
  Volume         = {35},
  Number         = {15},
  Pages          = {4867-4877},
  abstract       = {The backbone dynamics of the coiled-coil leucine
                   zipper domain of c-Jun have been studied using
                   proton-detected two-dimensional 1H-15N NMR
                   spectroscopy. Longitudinal (T1) and transverse (T2) 15N
                   relaxation times, together with \{1H\}15N NOEs, were
                   measured and analyzed by considering the protein to
                   approximate a prolate ellipsoid. An analysis of the
                   T1/T2 ratios for residues in the well-structured
                   section of the protein showed that a model for the
                   spectral density function in which the protein is
                   considered to reorient anisotropically fitted the data
                   significantly better than an isotropic model. Order
                   parameters (S2) in the range 0.7-0.9 were observed for
                   most residues, with lower values near the C-terminus,
                   consistent with fraying of the two helices comprising
                   the coiled-coil. Because nearly all of the N-H vectors
                   have small angles to the long axis of the molecule,
                   there was some uncertainty in the value of the
                   rotational diffusion coefficient Dpar, which describes
                   rotation about the long axis. Thus, an alternative
                   method was examined for its ability to provide
                   independent estimates of Dpar and Dperp (the diffusion
                   coefficient describing rotation about axes
                   perpendicular to the long axis); the transitional
                   diffusion coefficient (Dt) of the protein was measured,
                   and hydrodynamic calculations were used to predict Dpar
                   and Dperp. However, the derived rotational diffusion
                   coefficients proved to be very dependent on the
                   hydrodynamic model used to relate Dt to Dpar and Dperp,
                   and consequently the values obtained from the T1/T2
                   analysis were used in the order-paramenter analysis.
                   Although it has previously been reported that the side
                   chain of a polar residue at the dimer interface, Asn22,
                   undergoes a conformational exchange process and
                   destabilizes the dimer, no evidence of increased
                   backbone mobility in this region was detected,
                   suggesting that this process is confined to the Asn
                   side chain.},
  authoraddress  = {Department of Biochemistry, University of Sydney,
                   Australia.},
  keywords       = {Amino Acid Sequence ; *Leucine Zippers/genetics ;
                   Magnetic Resonance Spectroscopy ; Models, Chemical ;
                   Molecular Sequence Data ; Proto-Oncogene Proteins
                   c-jun/*chemistry/genetics ; Recombinant
                   Proteins/chemistry/genetics ; Research Support,
                   Non-U.S. Gov't},
  language       = {eng},
  doi            = {10.1021/bi952761y},
  medline-aid    = {10.1021/bi952761y [doi] ; bi952761y [pii]},
  medline-da     = {19960806},
  medline-dcom   = {19960806},
  medline-edat   = {1996/04/16},
  medline-fau    = {MacKay, J P ; Shaw, G L ; King, G F},
  medline-is     = {0006-2960},
  medline-jid    = {0370623},
  medline-lr     = {20041117},
  medline-mhda   = {1996/04/16 00:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {8664278},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Proto-Oncogene Proteins c-jun) ; 0 (Recombinant
                   Proteins)},
  medline-sb     = {IM},
  medline-so     = {Biochemistry 1996 Apr 16;35(15):4867-77.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=8664278},
  year           = 1996
}

@Article{Mandel96,
  Author         = {Mandel, A. M. and Akke, M. and Palmer, 3rd, A. G.},
  Title          = {Dynamics of ribonuclease {H}: {T}emperature dependence
                   of motions on multiple time scales},
  Journal        = biochem,
  Volume         = {35},
  Number         = {50},
  Pages          = {16009-16023},
  abstract       = {The temperature dependence of the backbone motions in
                   Escherichia coli ribonuclease HI was studied on
                   multiple time scales by 15N nuclear magnetic spin
                   relaxation. Laboratory frame relaxation data at 285,
                   300, and 310 K were analyzed using the model-free and
                   reduced spectral density approaches. The temperature
                   dependence of the order parameters was used to define a
                   characteristic temperature for the motions of the
                   backbone N-H bond vectors on picosecond to nanosecond
                   time scales. The characteristic temperatures for
                   secondary structure elements, loops, and the C-terminus
                   are approximately 1000, approximately 300, and
                   approximately 170 K, respectively. The observed
                   variation in the characteristic temperature indicates
                   that the energy landscape, and thus the configurational
                   heat capacity, is markedly structure dependent in the
                   folded protein. The effective correlation times for
                   internal motions do not show significant temperature
                   dependence. Conformational exchange was observed for a
                   large number of residues forming a contiguous region of
                   the protein that includes the coiled coil formed by
                   helices alpha A and alpha D. Exchange broadening in the
                   CPMG experiments decreased with increased temperature,
                   directly demonstrating that the microscopic exchange
                   rate is faster than the pulse repetition rate of 1.2
                   ms. The temperature dependence of the exchange
                   contributions to the transverse relaxation rate
                   constant shows approximately Arrhenius behavior over
                   the studied temperature range with apparent activation
                   enthalpies of approximately 20-50 kJ/mol. Numerical
                   calculations suggest that these values underestimate
                   the activation barriers by at most a factor of 2. The
                   present results obtained at 300 K are compared to those
                   reported previously [Mandel, A. M., Akke, M., \&
                   Palmer, A. G., III (1995) J. Mol. Biol. 246, 144-163]
                   to establish the reproducibility of the experimental
                   techniques.},
  authoraddress  = {Department of Biochemistry and Molecular Biophysics,
                   Columbia University, New York, New York 10032, USA.},
  keywords       = {Amino Acid Sequence ; Computer Simulation ;
                   Escherichia coli/*enzymology ; Kinetics ; Magnetic
                   Resonance Spectroscopy ; *Models, Chemical ; *Models,
                   Structural ; *Protein Structure, Secondary ;
                   Recombinant Proteins/chemistry ; Research Support,
                   Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S. ;
                   Ribonuclease H, Calf Thymus/*chemistry ; Thermodynamics},
  language       = {eng},
  doi            = {10.1021/bi962089k},
  medline-aid    = {10.1021/bi962089k [doi] ; bi962089k [pii]},
  medline-da     = {19970123},
  medline-dcom   = {19970123},
  medline-edat   = {1996/12/17},
  medline-fau    = {Mandel, A M ; Akke, M ; Palmer, A G 3rd},
  medline-gr     = {5T32-GM-07367/GM/NIGMS ; GM-50291/GM/NIGMS},
  medline-is     = {0006-2960},
  medline-jid    = {0370623},
  medline-lr     = {20041117},
  medline-mhda   = {2001/03/28 10:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {8973171},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Recombinant Proteins) ; EC 3.1.26.4 (Ribonuclease
                   H, Calf Thymus)},
  medline-sb     = {IM},
  medline-so     = {Biochemistry 1996 Dec 17;35(50):16009-23.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=8973171},
  year           = 1996
}

@Article{Mandel95,
  Author         = {Mandel, A. M. and Akke, M. and Palmer, 3rd, A. G.},
  Title          = {Backbone dynamics of {\em{E}scherichia coli}
                   ribonuclease {HI}: correlations with structure and
                   function in an active enzyme.},
  Journal        = jmb,
  Volume         = {246},
  Number         = {1},
  Pages          = {144-163},
  abstract       = {Ribonuclease H is an endonuclease that hydrolyzes the
                   RNA moiety of RNA-DNA duplex molecules. Escherichia
                   coli ribonuclease H is involved in DNA replication, and
                   retroviral ribonuclease H is essential for reverse
                   transcription of the viral genome. To characterize the
                   intramolecular dynamical properties of E. coli
                   ribonuclease H, spin-lattice relaxation rate constants,
                   spin-spin relaxation rate constants and steady state
                   nuclear Overhauser effects for the 15N nuclear spins
                   were measured by using proton-detected heteronuclear
                   NMR spectroscopy. The relaxation data were analyzed by
                   using a series of dynamical models in conjunction with
                   a statistical model selection protocol. Ribonuclease H
                   exhibits a complex array of dynamical features, most
                   notably in the parallel beta-strands of the principal
                   five-stranded beta-sheet, the coiled-coil helical
                   interface, the active site, and the loop regions
                   surrounding the active site. The dynamical properties
                   are correlated with local structural environments of
                   the 15N spins and suggest possible relationships to the
                   functional properties of ribonuclease H. Results for E.
                   coli ribonuclease H are compared to previously reported
                   results for the human immunodeficiency virus type 1
                   ribonuclease H domain of reverse transcriptase.},
  authoraddress  = {Department of Biochemistry and Molecular Biophysics,
                   Columbia University, New York, NY 10032.},
  keywords       = {Binding Sites ; Escherichia coli/*enzymology ;
                   HIV-1/enzymology ; HIV-1 Reverse Transcriptase ; Humans
                   ; Magnetic Resonance Spectroscopy ; *Models, Molecular
                   ; Molecular Structure ; *Protein Structure, Secondary ;
                   RNA-Directed DNA Polymerase/chemistry ; Research
                   Support, Non-U.S. Gov't ; Research Support, U.S. Gov't,
                   P.H.S. ; Ribonuclease H, Calf
                   Thymus/*chemistry/metabolism ; Structure-Activity
                   Relationship},
  language       = {eng},
  medline-aid    = {S0022283684700738 [pii]},
  medline-da     = {19950316},
  medline-dcom   = {19950316},
  medline-edat   = {1995/02/10},
  medline-fau    = {Mandel, A M ; Akke, M ; Palmer, A G 3rd},
  medline-gr     = {5T32-GM-07367/GM/NIGMS ; GM-50291/GM/NIGMS},
  medline-is     = {0022-2836},
  medline-jid    = {2985088R},
  medline-lr     = {20041117},
  medline-mhda   = {2001/03/28 10:01},
  medline-own    = {NLM},
  medline-pl     = {ENGLAND},
  medline-pmid   = {7531772},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {EC 2.7.7.- (HIV-1 Reverse Transcriptase) ; EC 2.7.7.49
                   (RNA-Directed DNA Polymerase) ; EC 3.1.26.4
                   (Ribonuclease H, Calf Thymus) ; EC 3.1.26.4
                   (ribonuclease HI)},
  medline-sb     = {IM ; X},
  medline-so     = {J Mol Biol 1995 Feb 10;246(1):144-63.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=7531772},
  year           = 1995,
  doi            = {10.1006/jmbi.1994.0073}
}

@Article{Marquardt63,
  Author         = {Marquardt, D. W.},
  Title          = {An algorithm for least squares estimation of
                   non-linear parameters},
  Journal        = siamj,
  Volume         = {11},
  Pages          = {431-441},
  doi            = {10.1137/0111030},
  year           = 1963
}

@Article{Mazur13,
  Author         = {Mazur, A. and Hammesfahr, B. and Griesinger, C. and
                   Lee, D. and Kollmar, M.},
  Title          = {Shere{K}han--calculating exchange parameters in
                   relaxation dispersion data from {CPMG} experiments.},
  Journal        = bioinformatics,
  Volume         = {29},
  Number         = {14},
  Pages          = {1819-1820},
  abstract       = {SUMMARY: Dynamics governing the function of
                   biomolecule is usually described as exchange processes
                   and can be monitored at atomic resolution with nuclear
                   magnetic resonance (NMR) relaxation dispersion data.
                   Here, we present a new tool for the analysis of CPMG
                   relaxation dispersion profiles (ShereKhan). The web
                   interface to ShereKhan provides a user-friendly
                   environment for the analysis. AVAILABILITY: A stable
                   version of ShereKhan, the web application and
                   documentation are available at
                   http://sherekhan.bionmr.org. CONTACT:
                   dole@nmr.mpibpc.mpg.de or mako@nmr.mpibpc.mpg.de.},
  authoraddress  = {Department of NMR-based Structural Biology,
                   Max-Planck-Institute for Biophysical Chemistry, Am
                   Fassberg 11, 37077 Gottingen, Germany.},
  language       = {eng},
  medline-aid    = {btt286 [pii] ; 10.1093/bioinformatics/btt286 [doi]},
  medline-crdt   = {2013/05/24 06:00},
  medline-da     = {20130708},
  medline-dep    = {20130521},
  medline-edat   = {2013/05/24 06:00},
  medline-fau    = {Mazur, Adam ; Hammesfahr, Bjorn ; Griesinger,
                   Christian ; Lee, Donghan ; Kollmar, Martin},
  medline-is     = {1367-4811 (Electronic) ; 1367-4803 (Linking)},
  medline-jid    = {9808944},
  medline-jt     = {Bioinformatics (Oxford, England)},
  medline-lid    = {10.1093/bioinformatics/btt286 [doi]},
  medline-mhda   = {2013/05/24 06:00},
  medline-own    = {NLM},
  medline-phst   = {2013/05/21 [aheadofprint] ; 2013/06/14 [aheadofprint]},
  medline-pl     = {England},
  medline-pmid   = {23698862},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-sb     = {IM},
  medline-so     = {Bioinformatics. 2013 Jul 15;29(14):1819-20. doi:
                   10.1093/bioinformatics/btt286. Epub 2013 May 21.},
  medline-stat   = {In-Data-Review},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=23698862},
  doi            = {10.1093/bioinformatics/btt286},
  year           = 2013
}

@Article{McConnell58,
  Author         = {McConnell, H.M.},
  Title          = {Reaction rates by nuclear magnetic resonance},
  Journal        = jcp,
  Volume         = {28},
  Number         = {3},
  Pages          = {430-431},
  address        = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD,
                   WOODBURY, NY 11797-2999},
  doc-delivery-number = {WA154},
  doi            = {10.1063/1.1744152},
  issn           = {0021-9606},
  journal-iso    = {J. Chem. Phys.},
  language       = {English},
  number-of-cited-references = {7},
  publisher      = {AMER INST PHYSICS},
  research-areas = {Physics},
  times-cited    = {1114},
  type           = {Article},
  unique-id      = {ISI:A1958WA15400013},
  web-of-science-categories = {Physics, Atomic, Molecular \& Chemical},
  year           = 1958
}

@Article{Meiboom61,
  Author         = {Meiboom, S.},
  Title          = {Nuclear magnetic resonance study of proton transfer
                   in water},
  Journal        = jcp,
  Volume         = {34},
  Number         = {2},
  Pages          = {375-388},
  address        = {Circulation Fulfillment Div, 500 Sunnyside Blvd,
                   Woodbury, NY 11797-2999},
  doc-delivery-number = {4113B},
  doi            = {10.1063/1.1700960},
  issn           = {0021-9606},
  journal-iso    = {J. Chem. Phys.},
  language       = {English},
  number-of-cited-references = {28},
  publisher      = {Amer Inst Physics},
  research-areas = {Physics},
  times-cited    = {488},
  type           = {Article},
  unique-id      = {ISI:A19614113B00052},
  web-of-science-categories = {Physics, Atomic, Molecular \& Chemical},
  year           = 1961
}

@Article{Millet00,
  Author         = {Millet, O. and Loria, J. P. and Kroenke, C. D. and
                   Pons, M. and Palmer, A. G.},
  Title          = {The static magnetic field dependence of chemical
                   exchange linebroadening defines the {NMR} chemical
                   shift time scale},
  Journal        = jacs,
  Volume         = {122},
  Number         = {12},
  Pages          = {2867-2877},
  abstract       = {The static magnetic field dependence of chemical
                   exchange linebroadening in NMR spectroscopy is
                   investigated theoretically and experimentally. Two-site
                   exchange (A reversible arrow B) is considered with site
                   A more highly populated than site B (p(a) > p(b)), a
                   shift difference between sites equal to aw, and an
                   exchange rate constant given by k(ex). The exchange
                   contribution to the transverse relaxation rate constant
                   for the more highly populated site is denoted R-ex. The
                   dependence of R-ex,, on the static magnetic field
                   strength is characterized by a scaling parameter alpha
                   = d In R-ex/d In Delta omega in which 0 less than or
                   equal to alpha less than or equal to 2 for p(a) > 0.7.
                   The value of alpha depends on the NMR chemical shift
                   time scale for the exchange process: for slow exchange
                   (k(ex)/Delta omega < 1), 0 less than or equal to alpha
                   < 1; for intermediate exchange (k(ex)/Delta omega > 1),
                   alpha = 1 and for fast exchange (k(ex)/Delta omega >
                   1), 1 < alpha less than or equal to 2. Consequently,
                   the static magnetic field dependence of R-ex defines
                   the chemical shift time scale for an exchange process
                   even if the populations are so highly skewed (p(a) much
                   greater than p(b)) that the minor resonance is not
                   observable in the slow exchange limit. The theoretical
                   results are verified by measuring '5N transverse
                   relaxation rate constants at static magnetic fields of
                   11.7 and 14.1 T and temperatures of 300 and 313 K fur
                   the protein basic pancreatic trypsin inhibitor. At each
                   combination of static magnetic field and temperature,
                   the rate constants were measured using
                   Carr-Purcel-Meiboom-Gill and Hahn echo techniques with
                   spin-echo delays ranging from 1.0 to 63.5 ms. '5N
                   resonances for residues in the region of the
                   Cys14-Cys38 disulfide bond are broadened due to
                   chemical exchange. Values of a obtained from the
                   relaxation rate constants range from 0.26 +/- 0.17 for
                   Arg39 at 300 K to 1.96 +/- 0.25 for Cys38 at 313 K. For
                   Cys38 and Arg39, the two residues most strongly
                   affected by chemical exchange, values of k(ex) were
                   determined to be 380 +/- 70 s(-1) and 530 +/- 90 s(-1)
                   at 300 K and 1300 +/- 290 s(-1) and 1370 +/- 160 s(-1)
                   at 313 K by global analysis of the relaxation rate
                   constants. The scaling parameters ex indicate that
                   chemical exchange for most residues in basic pancreatic
                   trypsin inhibitor does not satisfy k(ex) /Delta omega
                   much greater than 1. Consequently, the assumption of
                   fast-limit quadratic scaling of exchange broadening in
                   proteins and other macromolecules may be incorrect,
                   even if a single broadened resonance is observed for a
                   nuclear spin. The theoretical results for the static
                   magnetic field dependence of chemical exchange
                   broadening in NMR spectroscopy are applicable to other
                   nuclei and to other techniques for measuring chemical
                   exchange Linebroadening.},
  address        = {1155 16TH ST, NW, Washington, DC 20036 USA},
  authoraddress  = {Columbia Univ, Dept Biochem \& Mol Biophys, New York,
                   NY 10032 USA. ; Univ Barcelona, Dept Quim Organ,
                   E-08028 Barcelona, Spain.},
  citedref       = {AKKE M, 1996, J AM CHEM SOC, V118, P911 ; AKKE M,
                   1998, NAT STRUCT BIOL, V5, P55 ; ALEXANDRESCU AT, 1998,
                   PROTEIN SCI, V7, P389 ; BEESER SA, 1997, J MOL BIOL,
                   V269, P154 ; BESSER SA, 1998, J MOL BIOL, V284, P1581 ;
                   BRACKEN C, 1999, J MOL BIOL, V285, P2133 ; CARR HY,
                   1954, PHYS REV, V94, P630 ; CAVANAGH J, 1996, PROTEIN
                   NMR SPECTROS, P587 ; DAVIS DG, 1994, J MAGN RESON SER
                   B, V104, P266 ; DEVERELL C, 1970, MOL PHYS, V18, P553 ;
                   EVENAS J, 1999, J MOL BIOL, V289, P603 ; FARROW NA,
                   1995, BIOCHEMISTRY-US, V34, P868 ; FARROW NA, 1995, J
                   BIOMOL NMR, V6, P153 ; FRAUENFELDER H, 1991, SCIENCE,
                   V254, P1598 ; GLUSHKA J, 1989, J AM CHEM SOC, V111,
                   P7716 ; ISHIMA R, 1998, J AM CHEM SOC, V120, P10534 ;
                   ISHIMA R, 1999, J BIOMOL NMR, V15, P369 ; ISHIMA R,
                   1999, STRUCT FOLD DES, V7, P1047 ; JEN J, 1978, J MAGN
                   RESON, V30, P111 ; KARPLUS M, 1983, ANNU REV BIOCHEM,
                   V53, P263 ; KAY LE, 1992, J AM CHEM SOC, V114, P10663 ;
                   KAY LE, 1992, J MAGN RESON, V97, P359 ; KAY LE, 1998,
                   NAT STRUCT BIOL S, V5, P513 ; KAY LE, 1998, NAT STRUCT
                   BIOL, V5, P156 ; KONRAT R, 1999, J BIOMOL NMR, V13,
                   P213 ; KROENKE CD, 1998, J AM CHEM SOC, V120, P7905 ;
                   LORIA JP, 1999, J AM CHEM SOC, V121, P2331 ; LORIA JP,
                   1999, J BIOMOL NMR, V15, P151 ; LUZ Z, 1963, J CHEM
                   PHYS, V39, P366 ; MANDEL AM, 1995, J MOL BIOL, V246,
                   P144 ; MANDEL AM, 1996, BIOCHEMISTRY-US, V35, P16009 ;
                   MARION D, 1989, J MAGN RESON, V85, P393 ; MEIBOOM S,
                   1958, REV SCI INSTRUM, V29, P688 ; MEIBOOM S, 1961, J
                   CHEM PHYS, V34, P375 ; MOSTELLER F, 1977, DATA ANAL
                   REGRESSION ; MULDER FAA, 1999, J BIOMOL NMR, V13, P275
                   ; OREKHOV VY, 1994, EUR J BIOCHEM, V219, P887 ; OTTING
                   G, 1993, BIOCHEMISTRY-US, V32, P3571 ; PALMER AG, 1991,
                   J AM CHEM SOC, V113, P4371 ; PALMER AG, 1992, MOL PHYS,
                   V75, P699 ; PALMER AG, 1996, J PHYS CHEM-US, V100,
                   P13293 ; PALMER AG, 1997, CURR OPIN STRUC BIOL, V7,
                   P732 ; PENG JW, 1992, J MAGN RESON, V98, P308 ; PENG
                   JW, 1995, BIOCHEMISTRY-US, V34, P16733 ; PERVUSHIN K,
                   1997, P NATL ACAD SCI USA, V94, P12366 ; PHAN IQH,
                   1996, J BIOMOL NMR, V8, P369 ; SHAKA AJ, 1985, J MAGN
                   RESON, V64, P547 ; SKELTON NJ, 1993, J MAGN RESON SER
                   B, V102, P253 ; SZYPERSKI T, 1993, J BIOMOL NMR, V3,
                   P151 ; TJANDRA N, 1996, J AM CHEM SOC, V118, P6986 ;
                   WIDER G, 1991, J BIOMOL NMR, V1, P93 ; YANG DW, 1996, J
                   MOL BIOL, V263, P369 ; ZINNJUSTIN S, 1997, J BIOMOL
                   NMR, V10, P363},
  isifile-dt     = {Article},
  isifile-ga     = {299NL},
  isifile-j9     = {J Amer Chem Soc},
  isifile-ji     = {J. Am. Chem. Soc.},
  isifile-nr     = {53},
  isifile-pi     = {Washington},
  isifile-rp     = {Palmer, AG, Columbia Univ, Dept Biochem \& Mol
                   Biophys, 630 W 168th St, ; New York, NY 10032 USA.},
  isifile-sc     = {Chemistry, Multidisciplinary},
  isifile-tc     = {83},
  issn           = {0002-7863},
  keywords       = {[ISI:] backbone dynamics; heteronuclear nmr;
                   biological macromolecules; relaxation interference;
                   cross-correlation; protein dynamics; rotating frame;
                   motions; spectroscopy; anisotropy ;;},
  language       = {English},
  month          = {Mar 29},
  publisher      = {Amer Chemical Soc},
  size           = {11 p.},
  sourceid       = {ISI:000086204700023},
  year           = 2000
}

@Article{MiloushevPalmer05,
  Author         = {Miloushev, V. Z. and Palmer, 3rd, A. G.},
  Title          = {R(1rho) relaxation for two-site chemical exchange:
                   general approximations and some exact solutions.},
  Journal        = jmr,
  Volume         = {177},
  Number         = {2},
  Pages          = {221-227},
  abstract       = {Analytic expressions for the nuclear magnetic spin
                   relaxation rate constant for magnetization spin-locked
                   in the rotating reference frame under an applied
                   radiofrequency field, R(1rho), are obtained for
                   two-site chemical exchange. The theoretical approach is
                   motivated by Laguerre's method and obtains R(1rho) as
                   the root of a (p1,q1) Pade approximant. The general
                   formula for R(1rho) obtained by this approach is
                   substantially simpler than existing expressions and is
                   equally or slightly more accurate, in most cases. In
                   addition, particular solutions for the R(1rho) rate
                   constant are presented for two special cases: equal
                   populations of the two exchanging sites, or placement
                   of the radiofrequency carrier at the average resonance
                   frequency of the two sites. The solutions are exact
                   when the R1 and R2 relaxation rate constants are
                   identical, and nearly exact under realistic
                   experimental conditions.},
  authoraddress  = {Department of Biochemistry and Molecular Biophysics,
                   Columbia University, 630 West 168th Street, New York,
                   NY 10032, USA.},
  keywords       = {*Models, Chemical ; Nuclear Magnetic Resonance,
                   Biomolecular/*methods ; Proteins/chemistry},
  language       = {eng},
  medline-aid    = {S1090-7807(05)00249-1 [pii] ;
                   10.1016/j.jmr.2005.07.023 [doi]},
  medline-crdt   = {2005/09/07 09:00},
  medline-da     = {20051128},
  medline-dcom   = {20060228},
  medline-dep    = {20050906},
  medline-edat   = {2005/09/07 09:00},
  medline-fau    = {Miloushev, Vesselin Z ; Palmer, Arthur G 3rd},
  medline-gr     = {GM07367/GM/NIGMS NIH HHS/United States ;
                   GM59273/GM/NIGMS NIH HHS/United States},
  medline-is     = {1090-7807 (Print) ; 1090-7807 (Linking)},
  medline-jid    = {9707935},
  medline-jt     = {Journal of magnetic resonance (San Diego, Calif. :
                   1997)},
  medline-lr     = {20071114},
  medline-mhda   = {2006/03/01 09:00},
  medline-own    = {NLM},
  medline-phst   = {2005/04/29 [received] ; 2005/06/21 [revised] ;
                   2005/07/28 [accepted] ; 2005/09/06 [aheadofprint]},
  medline-pl     = {United States},
  medline-pmid   = {16143548},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article ; Research Support, N.I.H., Extramural},
  medline-rn     = {0 (Proteins)},
  medline-sb     = {IM},
  medline-so     = {J Magn Reson. 2005 Dec;177(2):221-7. Epub 2005 Sep 6.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=16143548},
  doi            = {10.1016/j.jmr.2005.07.023},
  year           = 2005
}

@Article{MoreThuente94,
  Author         = {Mor{\'e}, J. J. and Thuente, D. J.},
  Title          = {Line search algorithms with guaranteed sufficient
                   decrease},
  Journal        = acmtms,
  Volume         = {20},
  Number         = {3},
  Pages          = {286-307},
  abstract       = {The development of software for minimization problems
                   is often based on a line search method. We consider
                   line search methods that satisfy sufficient decrease
                   and curvature conditions, and formulate the problem of
                   determining a point that satisfies these two conditions
                   in terms of finding a point in a set T(mu). We describe
                   a search algorithm for this problem that produces a
                   sequence of iterates that converge to a point in T(mu)
                   and that, except for pathological cases, terminates in
                   a finite number of steps. Numerical results for an
                   implementation of the search algorithm on a set of test
                   functions show that the algorithm terminates within a
                   small number of iterations.},
  address        = {1515 BROADWAY, NEW YORK, NY 10036},
  authoraddress  = {INDIANA PURDUE UNIV,DEPT MATH SCI,FT WAYNE,IN 46805.},
  citedref       = {ALBAALI M, 1984, J OPTIM THEORY APPL, V48, P359 ;
                   ALBAALI M, 1985, IMA J NUMER ANAL, V5, P121 ; BYRD RH,
                   1987, SIAM J NUMER ANAL, V24, P1171 ; DENNIS JE, 1983,
                   NUMERICAL METHODS UN ; FLETCHER R, 1980, PRACTICAL
                   METHODS OP, V1 ; FLETCHER R, 1987, PRACTICAL METHODS OP
                   ; GILBERT JC, 1992, SIAM J OPTIMIZ, V2, P21 ; GILL PE,
                   1974, NAC37 NAT PHYS LAB R ; GILL PE, 1979, SOL7925
                   STANF U SYST ; HAGER WW, 1989, COMPUT MATH APPL, V18,
                   P779 ; LEMARECHAL C, 1981, LECTURE NOTES CONTRO, V30,
                   P59 ; LIU DC, 1989, MATH PROGRAM, V45, P503 ; MORE JJ,
                   1984, STUDIES NUMERICAL AN, P29 ; OLEARY DP, 1990, SIAM
                   J MATRIX ANAL A, V11, P466 ; POWELL MJD, 1976, SIAM AMS
                   P, V9, P53 ; SCHLICK T, 1992, ACM T MATH SOFTWARE, V18,
                   P46 ; SCHLICK T, 1992, ACM T MATH SOFTWARE, V18, P71 ;
                   SHANNO DF, 1976, ACM T MATH SOFTWARE, V2, P87 ; SHANNO
                   DF, 1980, ACM T MATH SOFTWARE, V6, P618 ; YANAI H,
                   1981, COMPUTING, V27, P155},
  isifile-dt     = {Article},
  isifile-ga     = {PR442},
  isifile-j9     = {ACM TRANS MATH SOFTWARE},
  isifile-nr     = {20},
  isifile-pi     = {NEW YORK},
  isifile-rp     = {MORE, JJ, ARGONNE NATL LAB,DIV MATH & COMP SCI,9700 S
                   CASS ; AVE,ARGONNE,IL 60439.},
  isifile-sc     = {Computer Science, Software Engineering; Mathematics,
                   Applied},
  isifile-tc     = {34},
  issn           = {0098-3500},
  keywords       = {ALGORITHMS; CONJUGATE GRADIENT ALGORITHMS; LINE SEARCH
                   ALGORITHMS; NONLINEAR OPTIMIZATION; TRUNCATED NEWTON
                   ALGORITHMS; VARIABLE METRIC ALGORITHMS ; [ISI:] newton
                   minimization package; large-scale problems; global
                   convergence; tnpack ;;},
  language       = {English},
  month          = {SEP},
  publisher      = {ASSOC COMPUTING MACHINERY},
  size           = {22 p.},
  sourceid       = {ISI:A1994PR44200004},
  doi            = {10.1145/192115.192132},
  year           = 1994
}

@Book{Nelson67,
  Author         = {Edward Nelson},
  Title          = {Dynamical Theories of {B}rownian Motion},
  Publisher      = {Princeton University Press},
  year           = 1967
}

@Book{NocedalWright99,
  Author         = {Nocedal, J. and Wright, S. J.},
  Title          = {Numerical Optimization},
  Publisher      = {Springer-Verlag},
  Series         = {Springer Series in Operations Research},
  Address        = {New York},
  description    = {Numerical Optimization presents a comprehensive and
                   up-to-date description of the most effective methods in
                   continuous optimization. It responds to the growing
                   interest in optimization in engineering, science, and
                   business by focusing on the methods that are best
                   suited to practical problems.. "Because of the emphasis
                   on practical methods, as well as the extensive
                   illustrations and exercises, the book is accessible to
                   a wide audience. It can be used as a graduate text in
                   engineering, operations research, mathematics, computer
                   science, and business. It also serves as a handbook for
                   researchers and practitioners in the field.},
  isbn           = {0387987932},
  pages          = {636},
  year           = 1999
}

@Article{Morin11,
  author = {Morin, S.},
  title = {A practical guide to protein dynamics from $^{15}${N} spin relaxation in solution},
  journal = pnmrs,
  year = {2011},
  volume = {59},
  number = {3},
  pages = {245-262},
  month = oct,
  doi = {10.1016/j.pnmrs.2010.12.003}
}

@Article{Morin14,
  author = {Morin, S. and Linnet, T. E. and Lescanne, M. and Schanda, P. and Thompson, G. S. and Tollinger, M. and Teilum, K. and Gagn\'e, S. and Marion, D. and Griesinger, C. and Blackledge, M. and d'Auvergne, E. J.},
  title = {relax: the analysis of biomolecular kinetics and thermodynamics using {NMR} relaxation dispersion data},
  journal = bioinformatics,
  abstract = {Nuclear Magnetic Resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy to use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the GUI, is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimisation time are granted by parallelisation for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another – using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis.Availability: The software relax is written in Python with C modules and is released under the GPLv3+ licence. Source code and precompiled binaries for all major operating systems are available from http://www.nmr-relax.com. Contact: edward@nmr-relax.com}, 
  url = {http://bioinformatics.oxfordjournals.org/content/early/2014/04/09/bioinformatics.btu166.abstract}, 
  eprint = {http://bioinformatics.oxfordjournals.org/content/early/2014/04/09/bioinformatics.btu166.full.pdf+html}, 
  doi = {10.1093/bioinformatics/btu166},
  year = {2014}
}

@Article{MorinGagne09a,
  author = {Morin, S. and Gagn{\'e}, S.},
  affiliation = {Université Laval Département de Biochimie et de Microbiologie and PROTEO Bureau 3252, 1030 Avenue de la Médecine Québec QC G1V 0A6 Canada},
  title = {Simple tests for the validation of multiple field spin relaxation data},
  journal = jbnmr,
  publisher = {Springer Netherlands},
  issn = {0925-2738},
  keyword = {Physics and Astronomy},
  pages = {361-372},
  volume = {45},
  issue = {4},
  url = {http://dx.doi.org/10.1007/s10858-009-9381-4},
  doi = {10.1007/s10858-009-9381-4},
  abstract = {15N spin relaxation data is widely used to extract detailed dynamic information regarding bond vectors such as the amide N-H bond of the protein backbone. Analysis is typically carried using the Lipari-Szabo model-free approach. Even though the original model-free equation can be determined from single field R1 , R2 and NOE , over-determination of more complex motional models is dependent on the recording of multiple field datasets. This is especially important for the characterization of conformational exchange which affects R2 in a field dependent manner. However, severe artifacts can be introduced if inconsistencies arise between experimental setups with different magnets (or samples). Here, we propose the use of simple tests as validation tools for the assessment of consistency between different datasets recorded at multiple magnetic fields. Synthetic data are used to show the effects of inconsistencies on the proposed tests. Moreover, an analysis of data currently deposited in the BMRB is performed. Finally, two cases from our laboratory are presented. These tests are implemented in the open-source program relax , and we propose their use as a routine check-up for assessment of multiple field dataset consistency prior to any analysis such as model-free calculations. We believe this will aid in the extraction of higher quality dynamics information from 15N spin relaxation data.},
  year = {2009}
}

@Article{MorinGagne09b,
  author = {Morin, S. and Gagn{\'e}, S. M.},
  title = {{NMR} dynamics of {PSE}-4 $\beta$-lactamase: An interplay of ps-ns order and $\mu$s-ms motions in the active site},
  journal = bj,
  year = {2009},
  volume = {96},
  number = {11},
  pages = {4681-4691},
  month = jun,
  doi = {10.1016/j.bpj.2009.02.068}
}

@Article{OConnell09,
  Author         = {O'Connell, N. E. and Grey, M. J. and Tang, Y. and
                   Kosuri, P. and Miloushev, V. Z. and Raleigh, D. P. and
                   Palmer, 3rd, A. G.},
  Title          = {Partially folded equilibrium intermediate of the
                   villin headpiece {HP}67 defined by 13{C} relaxation
                   dispersion.},
  Journal        = jbnmr,
  Volume         = {45},
  Number         = {1-2},
  Pages          = {85-98},
  abstract       = {Identification and characterization of ensembles of
                   intermediate states remains an important objective in
                   describing protein folding in atomic detail. The
                   67-residue villin headpiece, HP67, consists of an
                   N-terminal subdomain (residues 10-42) that transiently
                   unfolds at equilibrium under native-like conditions and
                   a highly stable C-terminal subdomain (residues 43-76).
                   The transition between folded and unfolded states of
                   the N-terminal domain has been characterized previously
                   by (15)N NMR relaxation dispersion measurements (Grey
                   et al. in J Mol Biol 355:1078, 2006). In the present
                   work, (13)C spin relaxation was used to further
                   characterize backbone and hydrophobic core
                   contributions to the unfolding process. Relaxation of
                   (13)C(alpha) spins was measured using the Hahn echo
                   technique at five static magnetic fields (11.7, 14.1,
                   16.4, 18.8, and 21.1 T) and the
                   Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion
                   method at a static magnetic field of 14.1 T. Relaxation
                   of methyl (13)C spins was measured using CPMG
                   relaxation dispersion experiments at static magnetic
                   fields of 14.1 and 18.8 T. Results for (13)C and (15)N
                   spins yielded a consistent model in which the partially
                   unfolded intermediate state of the N-terminal subdomain
                   maintains residual structure for residues near the
                   unprotonated His41 imidazole ring and in the interface
                   between the N- and C-terminal subdomains. In addition,
                   a second faster process was detected that appears to
                   represent local dynamics within the folded state of the
                   molecule and is largely confined to the hydrophobic
                   interface between the N- and C-terminal subdomains.},
  authoraddress  = {Department of Biochemistry and Molecular Biophysics,
                   Columbia University, 630 West 168th Street, New York,
                   NY 10032, USA.},
  keywords       = {Animals ; Carbon Isotopes/chemistry ; Chickens ;
                   Glycine/chemistry ; Kinetics ; Microfilament
                   Proteins/*chemistry ; Models, Molecular ; Nuclear
                   Magnetic Resonance, Biomolecular/*methods ; Peptide
                   Fragments/chemistry ; Protein Conformation ; Protein
                   Folding},
  language       = {eng},
  medline-aid    = {10.1007/s10858-009-9340-0 [doi]},
  medline-crdt   = {2009/08/01 09:00},
  medline-da     = {20090818},
  medline-dcom   = {20091020},
  medline-dep    = {20090731},
  medline-edat   = {2009/08/01 09:00},
  medline-fau    = {O'Connell, Nichole E ; Grey, Michael J ; Tang, Yuefeng
                   ; Kosuri, Pallav ; Miloushev, Vesselin Z ; Raleigh,
                   Daniel P ; Palmer, Arthur G 3rd},
  medline-gr     = {GM 59273/GM/NIGMS NIH HHS/United States ; GM
                   66354/GM/NIGMS NIH HHS/United States ; P41
                   GM066354-05/GM/NIGMS NIH HHS/United States ; R01
                   GM059273-11/GM/NIGMS NIH HHS/United States ; R01
                   GM059273-13/GM/NIGMS NIH HHS/United States ; T32 GM
                   008281/GM/NIGMS NIH HHS/United States ; T32
                   GM008281-22/GM/NIGMS NIH HHS/United States},
  medline-is     = {1573-5001 (Electronic) ; 0925-2738 (Linking)},
  medline-jid    = {9110829},
  medline-jt     = {Journal of biomolecular NMR},
  doi            = {10.1007/s10858-009-9340-0},
  medline-lid    = {10.1007/s10858-009-9340-0 [doi]},
  medline-lr     = {20130602},
  medline-mhda   = {2009/10/21 06:00},
  medline-mid    = {NIHMS167154},
  medline-oid    = {NLM: NIHMS167154 ; NLM: PMC2810208},
  medline-own    = {NLM},
  medline-phst   = {2009/06/11 [received] ; 2009/06/30 [accepted] ;
                   2009/07/31 [aheadofprint]},
  medline-pl     = {Netherlands},
  medline-pmc    = {PMC2810208},
  medline-pmid   = {19644656},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article ; Research Support, N.I.H., Extramural
                   ; Research Support, U.S. Gov't, Non-P.H.S.},
  medline-rn     = {0 (Carbon Isotopes) ; 0 (Microfilament Proteins) ; 0
                   (Peptide Fragments) ; 0 (villin) ; 56-40-6 (Glycine)},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR. 2009 Sep;45(1-2):85-98. doi:
                   10.1007/s10858-009-9340-0. Epub 2009 Jul 31.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=19644656},
  year           = 2009
}

@Article{Orekhov99b,
  Author         = {Orekhov, V. Y. and Korzhnev, D. M. and Diercks, T. and
                   Kessler, H. and Arseniev, A. S.},
  Title          = {{H}-1-{N}-15 {NMR} dynamic study of an isolated
                   alpha-helical peptide (1-36)bacteriorhodopsin reveals
                   the equilibrium helix-coil transitions},
  Journal        = jbnmr,
  Volume         = {14},
  Number         = {4},
  Pages          = {345-356},
  abstract       = {The backbone dynamics of the bacteriorhodopsin
                   fragment (1-36)BR solubilized in a 1:1
                   chloroform/methanol mixture were investigated by
                   heteronuclear H-1-N-15 NMR spectroscopy. The
                   heteronuclear N-15 longitudinal and transverse
                   relaxation rates and N-15\{H-1\} steady-state NOEs were
                   measured at three magnetic fields (11.7, 14.1, and 17.6
                   T). Careful statistical analysis resulted in the
                   selection of the extended model-free form of the
                   spectral density function [Clore et al. (1990) J. Am.
                   Chem. Soc., 112, 4989-4991] for all the backbone amides
                   of (1-36)BR. The peptide exhibits motions on the
                   micro-, nano-, and picosecond time scales. The dynamics
                   of the alpha-helical part of the peptide (residues
                   9-31) are characterised by nanosecond and picosecond
                   motions with mean order parameters S-s(2) = 0.60 and
                   S-f(2) = 0.84, respectively. The nanosecond motions
                   were attributed to the peptide's helix-coil transitions
                   in equilibrium. Residues 3-7 and 30-35 also exhibit
                   motions on the pico- and nanosecond time scales, but
                   with lower order parameters. Residue 10 at the
                   beginning of the alpha-helix and residues 30-35 at the
                   C-terminus are involved in conformational exchange
                   processes on the microsecond time scale. The
                   implications of the obtained results for the studies of
                   helix-coil transitions and the dynamics of membrane
                   proteins are discussed.},
  address        = {SPUIBOULEVARD 50, PO BOX 17, 3300 AA DORDRECHT,
                   NETHERLANDS},
  authoraddress  = {Russian Acad Sci, Shemyakin \& Ovchinnikov Inst
                   Bioorgan Chem, Moscow 117871, Russia. ; Univ
                   Gothenburg, Lundberg Lab, SE-40530 Gothenburg, Sweden.
                   ; Tech Univ Munich, Inst Organ Chem \& Biochem, D-85747
                   Garching, Germany.},
  citedref       = {ABRAGAM A, 1961, PRINCIPLES NUCL MAGN ; BALDWIN RL,
                   1989, TRENDS BIOCHEM SCI, V14, P291 ; BELOBORODOV IS,
                   1998, J MAGN RESON, V132, P328 ; BRACKEN C, 1999, J MOL
                   BIOL, V285, P2133 ; CHOU PY, 1971, BIOPOLYMERS, V10,
                   P657 ; CLORE GM, 1990, J AM CHEM SOC, V112, P4989 ;
                   CORDIER F, 1998, J MOL BIOL, V281, P341 ; DAGGETT V,
                   1992, J MOL BIOL, V223, P1121 ; DELATORRE JG, 1981, Q
                   REV BIOPHYS, V14, P81 ; FARROW NA, 1994,
                   BIOCHEMISTRY-US, V33, P5984 ; FUSHMAN D, 1998, J AM
                   CHEM SOC, V120, P7109 ; GRUENEWALD B, 1979, BIOPHYS
                   CHEM, V9, P137 ; HIROTA N, 1997, PROTEIN SCI, V6, P416
                   ; KAHN TW, 1992, BIOCHEMISTRY-US, V31, P6144 ; KARPLUS
                   M, 1994, PROTEIN SCI, V3, P650 ; KAY LE, 1989,
                   BIOCHEMISTRY-US, V28, P8972 ; KORZHNEV DM, 1997, J MAGN
                   RESON, V127, P184 ; KORZHNEV DM, 1999, J BIOMOL NMR,
                   V14, P357 ; KORZHNEV DM, 1999, J PHYS CHEM B, V103,
                   P7036 ; LIPARI G, 1982, J AM CHEM SOC, V104, P4546 ;
                   LUO PZ, 1997, BIOCHEMISTRY-US, V36, P8413 ; MANDEL AM,
                   1995, J MOL BIOL, V246, P144 ; MARTI T, 1998, J BIOL
                   CHEM, V273, P9312 ; MIICK SM, 1993, BIOCHEMISTRY-US,
                   V32, P8014 ; OREKHOV VY, 1995, APPL MAGN RESON, V9,
                   P581 ; OREKHOV VY, 1995, J BIOMOL NMR, V6, P113 ;
                   PALMER AG, 1996, J PHYS CHEM-US, V100, P13293 ;
                   PERVUSHIN KV, 1992, FEBS LETT, V308, P190 ; PERVUSHIN
                   KV, 1994, EUR J BIOCHEM, V219, P571 ; PERVUSHIN KV,
                   1995, BIOORG KHIM+, V21, P83 ; PERVUSHIN KV, 1995, J
                   BIOMOL NMR, V5, P383 ; PHILLIPS CM, 1995, P NATL ACAD
                   SCI USA, V92, P7292 ; POPOT JL, 1987, J MOL BIOL, V198,
                   P655 ; REEVES LW, 1975, DYNAMIC MAGNETIC RES, P83 ;
                   SCHOLTZ JM, 1992, ANNU REV BIOPH BIOM, V21, P95 ;
                   SCHURR JM, 1994, J MAGN RESON SER B, V105, P211 ;
                   THOMPSON PA, 1997, BIOCHEMISTRY-US, V36, P9200 ;
                   TJANDRA N, 1996, J BIOMOL NMR, V8, P273 ; VANGEET AL,
                   1970, ANAL CHEM, V42, P679 ; WILLIAMS S, 1996,
                   BIOCHEMISTRY-US, V35, P691 ; WOESSNER DE, 1962, J CHEM
                   PHYS, V37, P647},
  isifile-dt     = {Article},
  isifile-ga     = {234VK},
  isifile-j9     = {J Biomol NMR},
  isifile-ji     = {J. Biomol. NMR},
  isifile-nr     = {41},
  isifile-pi     = {Dordrecht},
  isifile-rp     = {Arseniev, AS, Russian Acad Sci, Shemyakin \&
                   Ovchinnikov Inst Bioorgan ; Chem, Ul Miklukho Maklaya
                   16-10, Moscow 117871, Russia.},
  isifile-sc     = {Biochemistry \& Molecular Biology; Spectroscopy},
  isifile-tc     = {12},
  issn           = {0925-2738},
  keywords       = {alpha helix; anisotropy; bacteriorhodopsin; CSA;
                   hydrogen bond; random coil; relaxation ; [ISI:]
                   nuclear-magnetic-resonance; model-free approach;
                   anisotropic rotational diffusion; backbone dynamics;
                   relaxation measurements; 3-dimensional structure;
                   molecular-dynamics; spectroscopy; proteins;
                   (1-71)bacterioopsin ;;},
  language       = {English},
  month          = {AUG},
  publisher      = {Kluwer Academic Publ},
  size           = {12 p.},
  sourceid       = {ISI:000082504900005},
  doi            = {10.1023/a:1008356809071},
  year           = 1999
}

@Article{Orekhov99a,
  Author         = {Orekhov, V. Y. and Korzhnev, D. M. and Pervushin, K.
                   V. and Hoffmann, E. and Arseniev, A. S.},
  Title          = {Sampling of protein dynamics in nanosecond time scale
                   by 15{N} {NMR} relaxation and self-diffusion
                   measurements.},
  Journal        = jbsd,
  Volume         = {17},
  Number         = {1},
  Pages          = {157-174},
  abstract       = {This paper presents a procedure for detection of
                   intermediate nanosecond internal dynamics in globular
                   proteins. The procedure uses 1H-15N relaxation
                   measurements at several spectrometer frequencies and
                   hydrodynamic calculations based on experimental
                   self-diffusion coefficients. New heteronuclear
                   experiments, using pulse field gradients, are
                   introduced for the measurement of translation diffusion
                   coefficients of 15N labeled proteins. An advanced
                   interpretation of recently published (Luginbuhl et al.,
                   Biochemistry, 36, 7305-7312 (1997)) backbone amide 15N
                   relaxation data, measured at two spectrometers (400 and
                   750 MHz for 1H) for N-terminal DNA-binding domain
                   (1-63) of 434 repressor, is presented.
                   Non-applicability of commonly used fast (picosecond)
                   dynamics model (FD) was justified by (i) poor fit of
                   relaxation data by the FD model-free spectral density
                   function both for isotropic and anisotropic models of
                   the overall molecular tumbling; (ii) specific
                   dependence of the overall rotation correlation times
                   calculated from T1/T2 ratio on the spectrometer
                   frequency; (iii) mismatch of the ratio of longitudinal
                   15N relaxation times T1, measured at different
                   spectrometer frequencies, in comparison with that
                   anticipated for the FD model; (iv) significantly
                   underestimated overall rotation correlation time
                   provided by the FD model (5.50+/-0.15 and 5.80+/-0.15
                   ns for 750 and 400 MHz spectrometer frequency
                   respectively) in comparison with correlation time
                   obtained from hydrodynamics. On the other hand, all
                   relaxation and hydrodynamics data are in good
                   correspondence with the model of intermediate
                   (nanoseconds) dynamics. Overall rotation correlation
                   time of 7.5+/-0.7 ns was calculated from experimental
                   translation self-diffusion rate using hydrodynamics
                   formalism (Garcia de la Torre, J. and Bloomfield, V. A.
                   Quart. Rev. Biophys., 14, 81-139 (1981)). The
                   statistical analysis of 15N relaxation data along with
                   the hydrodynamic consideration clearly revealed that
                   most of the residues in 434(1-63) repressor are
                   involved in the nanosecond internal dynamics
                   characterized by the the mean order parameters of
                   0.59+/-0.06 and the correlation times of ca. 5 ns.},
  authoraddress  = {Shemyakin and Ovchinnikov Institute of Bioorganic
                   Chemistry, Russian Academy of Sciences, Moscow.},
  keywords       = {Coliphages ; Computer Simulation ; *DNA-Binding
                   Proteins ; Diffusion ; Models, Molecular ; Nitrogen
                   Isotopes ; Nuclear Magnetic Resonance, Biomolecular ;
                   Protein Conformation ; Proteins/*chemistry ; Repressor
                   Proteins/chemistry ; Research Support, Non-U.S. Gov't ;
                   Time Factors},
  language       = {eng},
  medline-da     = {19991122},
  medline-dcom   = {19991122},
  medline-edat   = {1999/09/25},
  medline-fau    = {Orekhov, V Y ; Korzhnev, D M ; Pervushin, K V ;
                   Hoffmann, E ; Arseniev, A S},
  medline-is     = {0739-1102},
  medline-jid    = {8404176},
  medline-lr     = {20050322},
  medline-mhda   = {1999/09/25 00:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {10496429},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (DNA-Binding Proteins) ; 0 (Nitrogen Isotopes) ; 0
                   (Proteins) ; 0 (Repressor Proteins) ; 0 (bacteriophage
                   lambda repressor protein)},
  medline-sb     = {IM},
  medline-so     = {J Biomol Struct Dyn 1999 Aug;17(1):157-74.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=10496429},
  doi            = {10.1080/07391102.1999.10508348},
  year           = 1999
}

@Article{Orekhov95a,
  Author         = {Orekhov, V. Y. and Nolde, D. E. and Golovanov, A. P.
                   and Korzhnev, D. M. and Arseniev, A. S.},
  Title          = {Processing of heteronuclear {NMR} relaxation data with
                   the new software {DASHA}},
  Journal        = amr,
  Volume         = {9},
  Number         = {4},
  Pages          = {581-588},
  abstract       = {The new program DASHA is an efficient implementation
                   of common data processing steps for the protein
                   internal dynamic analysis. The ''model-free''
                   parameters and their uncertainties (Lipari G., Szabo
                   A.: J. Am. Chem. Sec. 104, 4546-559 (1982) can be
                   calculated from an arbitrary combination of
                   experimental data sets (i.e. heteronuclear H-1-N-15 or
                   H-1-C-13 relaxation times and NOE values at different
                   spectrometer frequencies). Anisotropy of the molecular
                   rotational diffusion could be also taken into account
                   without introduction of the new adjustable parameters
                   into the spectral density function J(omega), provided
                   the structure of the molecule is known. Parameters of
                   chemical (conformational) exchange can be estimated
                   from the CPMG spin-lock frequency dependences (Bloom et
                   al.: J. Chem. Phys. 42, 1615-1624 (1965); Orekhov et
                   al.: fur. J. Biochem. 219, 887-896 (1994). The program
                   can be used both in the interactive and batch modes. It
                   has sophisticated PostScript plotting facilities.},
  address        = {175 FIFTH AVE, NEW YORK, NY 10010},
  citedref       = {ABRAGAM A, 1961, PRINCIPLES NUCLEAR M ; BARBATO G,
                   1992, BIOCHEMISTRY-US, V31, P5269 ; BARCHI JJ, 1994,
                   PROTEIN SCI, V3, P15 ; BLOOM M, 1965, J CHEM PHYS, V42,
                   P1615 ; CARR HY, 1954, PHYS REV, V94, P630 ; CLORE GM,
                   1990, J AM CHEM SOC, V112, P4989 ; DELATORRE JG, 1977,
                   BIOPOLYMERS, V16, P1747 ; DELATORRE JG, 1977,
                   BIOPOLYMERS, V16, P1765 ; DELATORRE JG, 1981, Q REV
                   BIOPHYS, V14, P81 ; DEWERELL C, 1970, MOL PHYS, V18,
                   P553 ; HAPPEL J, 1973, LOW REYNOLDS NUMBER ; KAY LE,
                   1989, BIOCHEMISTRY-US, V28, P8972 ; LIPARI G, 1982, J
                   AM CHEM SOC, V104, P4546 ; OREKHOV VY, 1994, EUR J
                   BIOCHEM, V219, P887 ; OREKHOV VY, 1995, J BIOMOL NMR,
                   V6, P113 ; PALMER AG, 1991, J AM CHEM SOC, V113, P4371
                   ; REEVES LW, 1985, DYNAMIC NUCLEAR MAGN, P83 ; WAGNER
                   G, 1993, CURR OPIN STRUC BIOL, V3, P748 ; WOESSNER DE,
                   1962, J CHEM PHYS, V37, P647},
  isifile-dt     = {Letter},
  isifile-ga     = {TR350},
  isifile-j9     = {Appl Magn Reson},
  isifile-ji     = {Appl. Magn. Reson.},
  isifile-nr     = {19},
  isifile-pi     = {NEW YORK},
  isifile-rp     = {Orekhov, VY, Russian Acad Sci,Shemyakin \& Ovchinnikov
                   Inst Bioorgan ; Chem,UL Miklukho Maklaya 16-10,Moscow
                   117871,Russia.},
  isifile-sc     = {Physics, Atomic, Molecular \& Chemical; Spectroscopy},
  isifile-tc     = {39},
  issn           = {0937-9347},
  keywords       = {[ISI:] model-free approach; backbone dynamics;
                   spectroscopy; macromolecules; proteins ;;},
  language       = {English},
  publisher      = {Springer Verlag},
  size           = {8 p.},
  sourceid       = {ISI:A1995TR35000012},
  year           = 1995,
  doi            = {10.1007/bf03162365}
}

@Article{Orekhov95b,
  Author         = {Orekhov, V. Y. and Pervushin, K. V. and Korzhnev, D.
                   M. and Arseniev, A. S.},
  Title          = {Backbone dynamics of (1-71)Bacterioopsin and
                   (1-36)Bacterioopsin studied by 2-dimensional
                   {H}-1-{N}-15 {NMR}-spectroscopy},
  Journal        = jbnmr,
  Volume         = {6},
  Number         = {2},
  Pages          = {113-122},
  abstract       = {The backbone dynamics of uniformly N-15-labelled
                   fragments (residues 1-71 and 1-36) of bacterioopsin,
                   solubilized in two media (methanol-chloroform (1:1),
                   0.1 M (HCO2NH4)-H-2, or SDS micelles) have been
                   investigated using 2D proton-detected heteronuclear
                   H-1-N-15 NMR spectroscopy at two spectrometer
                   frequencies, 600 and 400 MHz. Contributions of the
                   conformational exchange to the transverse relaxation
                   rates of individual nitrogens were elucidated using an
                   set of different rates of the CPMG spin-lock pulse
                   train and were essentially suppressed by the
                   high-frequency CPMG spin-lock. We found that most of
                   the backbone amide groups of (1-71)bacterioopspin in
                   SDS micelles are involved in the conformational
                   exchange process over a rate range of 10(3) to 10(4)
                   s(-1). This conformational exchange is supposed to be
                   due to an interaction between two alpha-helixes of
                   (1-71)bacterioopsin, since the hydrolysis of the
                   peptide bond in the loop region results in the
                   disappearance of exchange line broadening. N-15
                   relaxation rates and H-1-N-15 NOE values were
                   interpreted using the model-free approach of Lipari and
                   Szabo [Lipari, G. and Szabo, A (1982). J Am. Chem.
                   Soc., 104, 4546-4559]. In addition to overall rotation
                   of the molecule, the backbone N-H vectors of the
                   peptides are involved in two types of internal motions:
                   fast, on a time scale <20 ps, and intermediate, on a
                   time scale close to 1 ns. The intermediate dynamics in
                   the alpha-helical stretches was mostly attributed to
                   bending motions. A decrease in the order parameter of
                   intermediate motions was also observed for residues
                   next to Pro(50), indicating an anisotropy of the
                   overall rotational diffusion of the molecule.
                   Distinctly mobile regions are identified by a large
                   decrease in the order parameter of intermediate motions
                   and correspond to the N- and C-termini, and to a loop
                   connecting the alpha-helixes of (1-71)bacterioopsin.
                   The internal dynamics of the alpha-helixes on the
                   millisecond and nanosecond time scales should be taken
                   into account in the development of a model of the
                   functioning bacteriorhodopsin.},
  address        = {PO Box 214, 2300 AE Leiden, Netherlands},
  authoraddress  = {Russian Acad Sci,Shemyakin \& Ovchinnikov Inst
                   Bioorgan Chem,Moscow 117871,Russia.},
  citedref       = {ABDULAEVA GV, 1987, BIOORG KHIM, V4, P1254 ; ABDULAEVA
                   GV, 1991, BIOL MEMBRANY, V8, P30 ; ABRAGAM A, 1961,
                   PRINCIPLES NUCLEAR M ; ARSENIEV AS, 1987, FEBS LETT,
                   V213, P283 ; ARSENIEV AS, 1988, FEBS LETT, V231, P81 ;
                   BARCHI JJ, 1994, PROTEIN SCI, V3, P15 ; BARSUKOV IL,
                   1992, EUR J BIOCHEM, V2206, P665 ; BAX A, 1989, METHOD
                   ENZYMOL, V176, P134 ; BLOOM M, 1965, J CHEM PHYS, V42,
                   P1615 ; CLORE GM, 1990, BIOCHEMISTRY-US, V29, P7387 ;
                   CLORE GM, 1990, J AM CHEM SOC, V112, P4989 ; CRESPI HL,
                   1982, METHOD ENZYMOL, V88, P3 ; DRAHEIM JE, 1991,
                   BIOPHYS J, V60, P89 ; GRASBERGER BL, 1993, J MOL BIOL,
                   V230, P364 ; HENDERSON R, 1990, J MOL BIOL, V213, P899
                   ; KAY LE, 1989, BIOCHEMISTRY-US, V89, P8972 ; LIPARI G,
                   1982, J AM CHEM SOC, V104, P4546 ; LOMIZE AL, 1992, J
                   BIOMOL NMR, V2, P361 ; MASLENNIKOV IV, 1990, BIOL
                   MEMBRANY, V8, P222 ; MASLENNIKOV IV, 1991, BIOL
                   MEMBRANY, V8, P156 ; MASLENNIKOV IV, 1991, BIOORG KHIM,
                   V17, P1456 ; MASLENNIKOV IV, 1993, BIOORG KHIM, V19, P5
                   ; OREKHOV VY, 1992, EUR J BIOCHEM, V210, P223 ; OREKHOV
                   VY, 1994, EUR J BIOCHEM, V219, P887 ; OVCHINNIKOV YA,
                   1982, FEBS LETT, V148, P179 ; PALMER AG, 1991, J AM
                   CHEM SOC, V113, P4371 ; PALMER AG, 1992, J AM CHEM SOC,
                   V114, P9059 ; PALMER AG, 1992, MOL PHYS, V75, P699 ;
                   PENG JW, 1992, J MAGN RESON, V98, P308 ; PERVUSHIN KV,
                   1991, J BIOMOL NMR, V1, P313 ; PERVUSHIN KV, 1992, FEBS
                   LETT, V308, P190 ; PERVUSHIN KV, 1992, MOL BIOL, V6,
                   P1397 ; PERVUSHIN KV, 1994, EUR J BIOCHEM, V219, P571 ;
                   PERVUSHIN KV, 1995, J BIOMOL NMR, V5, P383 ; POPOT JL,
                   1993, CURR OPIN STRUC BIOL, V3, P532 ; REEVES LW, 1975,
                   DYNAMIC MAGNETIC RES, P83 ; SEIGNEURET M, 1991, J BIOL
                   CHEM, V266, P10066 ; SEIGNEURET M, 1992, 5TH INT C RET
                   PROT D ; SOBOL AG, 1992, J BIOMOL NMR, V2, P161 ;
                   STATES DJ, 1982, J MAGN RESON, V48, P286 ; TORRES J,
                   1993, FEBS LETT, V318, P77 ; WAGNER G, 1993, CURR OPIN
                   STRUC BIOL, V3, P748 ; WOESSNER DE, 1962, J CHEM PHYS,
                   V37, P647 ; WOESSNER DE, 1969, J CHEM PHYS, V50, P719},
  isifile-dt     = {Article},
  isifile-ga     = {RY392},
  isifile-j9     = {J Biomol NMR},
  isifile-ji     = {J. Biomol. NMR},
  isifile-nr     = {44},
  isifile-pi     = {Leiden},
  isifile-sc     = {Biochemistry \& Molecular Biology; Spectroscopy},
  isifile-tc     = {24},
  issn           = {0925-2738},
  keywords       = {Bacteriorhodopsin; Conformational exchange; Dynamics;
                   Helix helix interaction; Micelles; Relaxation; Spatial
                   structure ; [ISI:] model-free approach; protein
                   bacteriorhodopsin; conformational dynamics; relaxation
                   measurements; secondary structure; bacterioopsin ;;},
  language       = {English},
  month          = {Sep},
  publisher      = {Escom Sci Publ BV},
  size           = {10 p.},
  sourceid       = {ISI:A1995RY39200001},
  doi            = {10.1007/BF00211774},
  year           = 1995
}

@Article{OsborneWright01,
  Author         = {Osborne, M. J. and Wright, P. E.},
  Title          = {Anisotropic rotational diffusion in model-free
                   analysis for a ternary {DHFR} complex.},
  Journal        = jbnmr,
  Volume         = {19},
  Number         = {3},
  Pages          = {209-230},
  abstract       = {Model-free analysis has been extensively used to
                   extract information on motions in proteins over a wide
                   range of timescales from NMR relaxation data. We
                   present a detailed analysis of the effects of
                   rotational anisotropy on the model-free analysis of a
                   ternary complex for dihydrofolate reductase (DHFR). Our
                   findings show that the small degree of anisotropy
                   exhibited by DHFR (Dparallel/Dperpendicular = 1.18)
                   introduces erroneous motional models, mostly exchange
                   terms, to over 50\% of the NH spins analyzed when
                   isotropic tumbling is assumed. Moreover, there is a
                   systematic change in S2, as large as 0.08 for some
                   residues. The significant effects of anisotropic
                   rotational diffusion on model-free motional parameters
                   are in marked contrast to previous studies and are
                   accentuated by lowering of the effective correlation
                   time using isotropic tumbling methods. This is caused
                   by the preponderance of NH vectors aligned
                   perpendicular to the principal diffusion tensor axis
                   and is readily detected because of the high quality of
                   the relaxation data. A novel procedure, COPED
                   (COmparison of Predicted and Experimental Diffusion
                   tensors) is presented for distinguishing genuine
                   motions from the effects of anisotropy by comparing
                   experimental relaxation data and data predicted from
                   hydrodynamic analyses. The procedure shows excellent
                   agreement with the slow motions detected from the
                   axially symmetric model-free analysis and represents an
                   independent procedure for determining rotational
                   diffusion and slow motions that can confirm or refute
                   established procedures that rely on relaxation data.
                   Our findings show that neglect of even small degrees of
                   rotational diffusion anisotropy can introduce
                   significant errors in model-free analysis when the data
                   is of high quality. These errors can hinder our
                   understanding of the role of internal motions in
                   protein function.},
  authoraddress  = {Department of Molecular Biology and Skaggs Institute
                   for Chemical Biology, The Scripps Research Institute,
                   La Jolla, CA 92037, USA.},
  keywords       = {Anisotropy ; Diffusion ; Folic Acid/*chemistry ;
                   Models, Chemical ; Models, Molecular ; Motion ;
                   Niacinamide/*analogs \& derivatives/*chemistry ;
                   Nuclear Magnetic Resonance, Biomolecular/*methods ;
                   Research Support, U.S. Gov't, P.H.S. ; Tetrahydrofolate
                   Dehydrogenase/*chemistry},
  language       = {eng},
  medline-da     = {20010501},
  medline-dcom   = {20011018},
  medline-edat   = {2001/05/02 10:00},
  medline-fau    = {Osborne, M J ; Wright, P E},
  medline-gr     = {GM56879/GM/NIGMS},
  medline-is     = {0925-2738},
  medline-jid    = {9110829},
  medline-lr     = {20041117},
  medline-mhda   = {2001/10/19 10:01},
  medline-own    = {NLM},
  medline-pl     = {Netherlands},
  medline-pmid   = {11330809},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (dihydronicotinamide) ; 59-30-3 (Folic Acid) ;
                   98-92-0 (Niacinamide) ; EC 1.5.1.3 (Tetrahydrofolate
                   Dehydrogenase)},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR 2001 Mar;19(3):209-30.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=11330809},
  year           = 2001
}

@Article{Palmer91,
  Author         = {Palmer, A. G. and Rance, M. and Wright, P. E.},
  Title          = {Intramolecular motions of a zinc finger {DNA}-binding
                   domain from {X}fin characterized by proton-detected
                   natural abundance {C}-12 heteronuclear
                   {NMR}-spectroscopy},
  Journal        = jacs,
  Volume         = {113},
  Number         = {12},
  Pages          = {4371-4380},
  abstract       = {The zinc finger DNA-binding domain Xfin-31 is a
                   25-residue peptide that binds a single zinc atom and
                   forms a compact globular structure in solution. To
                   characterize the intramolecular dynamics of Xfin-31,
                   the C-13 spin-lattice and spin-spin relaxation rate
                   constants and the \{H-1\}-C-13 nuclear Overhauser
                   effect (NOE) enhancements have been measured for the
                   backbone and side chain methine carbons by
                   two-dimensional proton-detected heteronuclear NMR
                   spectroscopy at a C-13 Larmor frequency of 125 MHz and
                   natural C-13 abundance. The relaxation rate constants
                   and the NOE enhancements have been analyzed by using a
                   model-free formalism that depends on the overall
                   rotational correlation time of the molecule, tau-m, the
                   order parameter S, and effective internal correlation
                   time, tau-e, for each methine carbon. The optimized
                   global value of tau-m is 1.88 +/- 0.02 ns. The backbone
                   C-alpha carbons are grouped into four categories based
                   on the values of the order parameters: the N-terminal
                   residue Tyr1 with S2 = 0.73 +/- 0.04; the C-terminal
                   residues Lys24 and Asn25 with S2 < 0.5; residues
                   Phe10-Lysl3 with an average S2 = 0.77 +/- 0.03; and the
                   remainder of the backbone carbon nuclei with an average
                   S2 = 0.89 +/- 0.05. For the side chain C-beta of Val11
                   and Val22 and the C-gamma of Leu5, the values of S2 are
                   0.62 +/- 0.03, 0.66 +/- 0.04, and 0.47 +/- 0.03,
                   respectively. Estimates of tau-e could be obtained for
                   13 of the backbone and 3 of the side chain methine
                   carbons. Excluding the terminal residues, the average
                   value of tau-e for the backbone carbon nuclei was 34
                   +/- 16 ps. With the exception of the terminal residues,
                   the motions of the backbone carbon nuclei of Xfin-31
                   are highly restricted. Residues 10-13, which form a
                   turn between the beta-sheet and the helix present in
                   the three-dimensional structure of Xfin-31, have a
                   slightly higher mobility than the rest of the interior
                   backbone, and the two residues at the C-terminus have
                   considerable conformational flexibility. The side
                   chains of the hydrophobic Val and Leu residues are more
                   mobile than the backbone but are still significantly
                   restricted, which indicates that Xfin-31 is compact
                   despite its small size. Systematically large spin-spin
                   relaxation rates for residues in the zinc binding site
                   imply that conformational exchange may occur in this
                   region on a time scale longer than the overall
                   rotational correlation time.},
  address        = {1155 16TH ST, NW, Washington, DC 20036},
  authoraddress  = {Scripps Res Inst, Res Inst, Dept Molec Biol, 10666 N
                   Torrey Pines Rd, LA Jolla, CA 92037 USA.},
  citedref       = {ABRAGAM A, 1961, PRINCIPLES NUCL MAGN, P264 ; ALGER
                   JR, 1984, Q REV BIOPHYS, V17, P83 ; ALLERHAND A, 1971,
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                   1965, J CHEM PHYS, V42, P1615 ; BOROWIAK DS, 1989,
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                   AM CHEM SOC, V112, P4989 ; CUSACK S, 1986, COMM MOL
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                   RESON, V64, P547 ; SKLENAR V, 1987, J MAGN RESON, V73,
                   P375 ; TORREY HC, 1956, PHYS REV, V104, P563 ; VOLD RL,
                   1968, J CHEM PHYS, V48, P3831 ; WAGNER G, 1983, Q REV
                   BIOPHYS, V16, P1 ; WEAVER AJ, 1988, BIOPHYS J, V54, P1
                   ; WELCH GR, 1982, PROG BIOPHYS MOL BIO, V39, P109 ;
                   WILLIAMS RJP, 1989, EUR J BIOCHEM, V183, P479 ; WODAK
                   SJ, 1987, PROG BIOPHYS MOL BIO, V49, P29 ; ZANG LH,
                   1990, BIOCHEMISTRY-US, V29, P6815},
  isifile-dt     = {Article},
  isifile-ga     = {FP844},
  isifile-j9     = {J Amer Chem Soc},
  isifile-ji     = {J. Am. Chem. Soc.},
  isifile-nr     = {91},
  isifile-pi     = {Washington},
  isifile-sc     = {Chemistry, Multidisciplinary},
  isifile-tc     = {384},
  issn           = {0002-7863},
  keywords       = {[ISI:] nuclear-magnetic-resonance; model-free
                   approach; pancreatic trypsin-inhibitor; chemical
                   shielding tensors; relaxation-times;
                   molecular-dynamics; backbone dynamics; staphylococcal
                   nuclease; polarization transfer; coupling-constants ;;},
  language       = {English},
  month          = {Jun 5},
  publisher      = {Amer Chemical Soc},
  size           = {10 p.},
  sourceid       = {ISI:A1991FP84400001},
  year           = 1991,
  doi            = {10.1021/ja00012a001}
}

@Article{PalmerMassi06,
  Author         = {Palmer, 3rd, A. G. and Massi, F.},
  Title          = {Characterization of the dynamics of biomacromolecules
                   using rotating-frame spin relaxation {NMR}
                   spectroscopy.},
  Journal        = cr,
  Volume         = {106},
  Number         = {5},
  Pages          = {1700-1719},
  authoraddress  = {Department of Biochemistry and Molecular Biophysics,
                   Columbia University, 630 West 168th Street, New York,
                   New York 10032, USA. agp6@columbia.edu},
  keywords       = {Kinetics ; Ligands ; Macromolecular
                   Substances/chemistry ; Magnetic Resonance
                   Spectroscopy/methods ; *Models, Chemical ; Molecular
                   Structure ; Multiprotein Complexes/chemistry ; Protein
                   Conformation ; Water/chemistry},
  language       = {eng},
  medline-aid    = {10.1021/cr0404287 [doi]},
  medline-crdt   = {2006/05/11 09:00},
  medline-da     = {20060510},
  medline-dcom   = {20071113},
  medline-edat   = {2006/05/11 09:00},
  medline-fau    = {Palmer, Arthur G 3rd ; Massi, Francesca},
  medline-gr     = {GM59273/GM/NIGMS NIH HHS/United States},
  medline-is     = {0009-2665 (Print) ; 0009-2665 (Linking)},
  medline-jid    = {2985134R},
  medline-jt     = {Chemical reviews},
  medline-lr     = {20071203},
  medline-mhda   = {2007/11/14 09:00},
  medline-own    = {NLM},
  medline-pl     = {United States},
  medline-pmid   = {16683750},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article ; Research Support, N.I.H., Extramural
                   ; Review},
  medline-rf     = {78},
  medline-rn     = {0 (Ligands) ; 0 (Macromolecular Substances) ; 0
                   (Multiprotein Complexes) ; 7732-18-5 (Water)},
  medline-sb     = {IM},
  medline-so     = {Chem Rev. 2006 May;106(5):1700-19.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=16683750},
  doi            = {10.1021/cr0404287},
  year           = 2006
}

@Article{Pawley01,
  Author         = {Pawley, N. H. and Wang, C. and Koide, S. and
                   Nicholson, L. K.},
  Title          = {An improved method for distinguishing between
                   anisotropic tumbling and chemical exchange in analysis
                   of 15{N} relaxation parameters.},
  Journal        = jbnmr,
  Volume         = {20},
  Number         = {2},
  Pages          = {149-165},
  abstract       = {Although an accurate description of global tumbling of
                   a protein is essential for correct analysis of internal
                   motions. proper distinction between the effects of
                   anisotropic rotational diffusion and conformational
                   exchange has remained a challenge. We present a novel
                   two-part filtering procedure designed specifically to
                   distinguish between the effects of anisotropy and
                   conformational exchange. The efficacy of this method is
                   assessed using synthetic data sets. The method is then
                   applied to two proteins of dramatically different size
                   and shape, OspA and SH3. The large size and extreme
                   anisotropy of OspA provide a challenging case, where
                   conformational exchange is a small perturbation of the
                   effects of anisotropy on transverse relaxation rates.
                   Conversely, in the chicken c-Src SH3 domain, with its
                   small size and nearly spherical shape, anisotropy is a
                   small perturbation of the effects of conformational
                   exchange on transverse relaxation rates. Accurate
                   extraction of the global tumbling parameters for each
                   protein allows optimal characterization of
                   conformational exchange processes, as well as ps-ns
                   time scale motions.},
  authoraddress  = {Department of Molecular Biology and Genetics, Cornell
                   University, Ithaca, NY 14853, USA.},
  keywords       = {Animals ; Anisotropy ; Antigens, Surface/chemistry ;
                   Bacterial Outer Membrane Proteins/chemistry ;
                   Crystallography, X-Ray ; *Lipoproteins ; Models,
                   Molecular ; Nitrogen Isotopes ; Nuclear Magnetic
                   Resonance, Biomolecular/*methods ; Protein Conformation
                   ; Proteins/*chemistry ; Research Support, Non-U.S.
                   Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ;
                   Research Support, U.S. Gov't, P.H.S. ; src Homology
                   Domains},
  language       = {eng},
  medline-da     = {20010809},
  medline-dcom   = {20020131},
  medline-edat   = {2001/08/10 10:00},
  medline-fau    = {Pawley, N H ; Wang, C ; Koide, S ; Nicholson, L K},
  medline-gr     = {R01-GM57215/GM/NIGMS},
  medline-is     = {0925-2738},
  medline-jid    = {9110829},
  medline-lr     = {20041117},
  medline-mhda   = {2002/02/01 10:01},
  medline-own    = {NLM},
  medline-pl     = {Netherlands},
  medline-pmid   = {11495246},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Antigens, Surface) ; 0 (Bacterial Outer Membrane
                   Proteins) ; 0 (Lipoproteins) ; 0 (Nitrogen Isotopes) ;
                   0 (OspA protein) ; 0 (Proteins)},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR 2001 Jun;20(2):149-65.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=11495246},
  year           = 2001
}

@Article{Perrin34,
  Author         = {Perrin, F.},
  Title          = {Mouvement {B}rownien d'un ellipso\"ide ({I}).
                   {D}ispersion di\'eletrique pour des mol\'ecules
                   ellipso\"idales},
  Journal        = jpr,
  Volume         = {5},
  Pages          = {497-511},
  address        = {7, Ave du Hoggar, Parc D Activites Courtaboeuf, BP
                   112, F-91944 Les ; Ulis Cedexa, France},
  citedref       = {DEBYE P, 1929, POLAR MOLEKELN ; DEHAASLORENTZ GL,
                   1913, BROWNSCHE BEWEGUNG ; EDWARDES D, 1892, Q J MATH,
                   V26, P70 ; EINSTEIN A, 1905, ANN PHYS-BERLIN, V17, P549
                   ; EINSTEIN A, 1906, ANN PHYS-BERLIN, V19, P289 ;
                   EINSTEIN A, 1906, ANN PHYS-BERLIN, V19, P289 ; EISTEIN
                   A, 1906, ANN PHYS, V19, P289 ; EISTEIN, 1910, ANN PHYS,
                   V33, P1105 ; LANGEVIN P, 1908, CR HEBD ACAD SCI, V146,
                   P530 ; OBERBECK A, 1876, J REINE ANGEW MATH, V81, P62 ;
                   PERRIN F, 1928, ANN SCI ECOLE NORM S, V45, P1 ; PERRIN
                   P, 1929, ANN PHYS, V12, P169},
  isifile-dt     = {Article},
  isifile-ga     = {V23ZV},
  isifile-j9     = {J Phys Radium},
  isifile-ji     = {J. Phys. Radium},
  isifile-nr     = {12},
  isifile-pi     = {Les Ulis Cedexa},
  isifile-sc     = {Physics, Multidisciplinary},
  isifile-tc     = {1311},
  issn           = {0368-3842},
  language       = {French},
  publisher      = {E D P Sciences},
  size           = {15 p.},
  sourceid       = {ISI:000201621900071},
  doi            = {10.1051/jphysrad:01934005010049700},
  year           = 1934
}

@Article{Perrin36,
  Author         = {Perrin, F.},
  Title          = {Mouvement {B}rownien d'un ellipso\"ide ({II}).
                   {R}otation libre et d\'epolarisation des fluorescences.
                   {T}ranslation et diffusion de mol\'ecules
                   ellipso\"idales},
  Journal        = jpr,
  Volume         = {7},
  Pages          = {1-11},
  address        = {7, Ave du Hoggar, Parc D Activites Courtaboeuf, BP
                   112, F-91944 Les ; Ulis Cedexa, France},
  citedref       = {CAHEN J, 1933, J CH PHYS, V30, P420 ; PERRIN F, 1926,
                   J PHYS-PARIS, V7, P390 ; PERRIN F, 1929, ANN PHYS, V12,
                   P169 ; PERRIN F, 1934, J PHYS-PARIS, V5, P497 ;
                   PRZIBRAM K, HDB EXP PHYS, V8, P702 ; PRZIBRAM K, 1911,
                   WIEN BER, V128, P1205 ; PRZIBRAM K, 1912, WIEN BER,
                   V121, P2347 ; PRZIBRAM K, 1913, WIEN BER, V122, P1895 ;
                   SOLEILLET P, 1929, ANN PHYS-PARIS, V12, P23},
  isifile-dt     = {Article},
  isifile-ga     = {V23ZX},
  isifile-j9     = {J Phys Radium},
  isifile-ji     = {J. Phys. Radium},
  isifile-nr     = {9},
  isifile-pi     = {Les Ulis Cedexa},
  isifile-sc     = {Physics, Multidisciplinary},
  isifile-tc     = {935},
  issn           = {0368-3842},
  language       = {French},
  publisher      = {E D P Sciences},
  size           = {11 p.},
  sourceid       = {ISI:000201622100001},
  doi            = {10.1051/jphysrad:01936007010100},
  year           = 1936
}

@Article{PolakRibiere69,
  Author         = {Polak, E. and Ribi{\`e}re, G.},
  Title          = {Note sur la convergence de m{\'e}thodes de directions
                   conjugu{\'e}es},
  Journal        = {Revue Fran{\c c}aise d'Informatique et de Recherche
                   Op{\'e}rationnelle},
  Volume         = {16},
  Pages          = {35-43},
  year           = 1969
}

@Article{Schurr94,
  Author         = {Schurr, J. M. and Babcock, H. P. and Fujimoto, B. S.},
  Title          = {A test of the model-free formulas. {E}ffects of
                   anisotropic rotational diffusion and dimerization.},
  Journal        = jmrb,
  Volume         = {105},
  Number         = {3},
  Pages          = {211-224},
  abstract       = {The effects of anisotropy of rotational diffusion and
                   extent of dimerization on the performance of the simple
                   and extended model-free formulas are investigated.
                   Numerically exact 15N NMR R1, R2, and NOE data are
                   simulated for cylindrically symmetric species and also
                   for mixtures of spherical monomers and dimers with the
                   same internal dynamics. The relevant internuclear
                   vectors are assumed to move in isotropic deflection
                   potentials fixed at different orientations in the
                   molecule and to exhibit a single relaxation time in
                   their internal correlation functions. The simple
                   model-free formula is fitted to these simulated data in
                   order to obtain the best-fit order parameter and
                   internal relaxation time for each nucleus. Fitting is
                   accomplished by the standard data-analysis protocol, in
                   which a single common global correlation time is
                   adjusted, and also by an alternative protocol, in which
                   the global correlation time is adjusted separately for
                   each nucleus. The extended model-free formula is
                   likewise fitted to these same data. With noise-free
                   data, the simple model-free formula and standard
                   protocol yield remarkably good best-fit internal motion
                   parameters up to moderate anisotropies (r = D
                   parallel/D perpendicular = 2.0), but some or many of
                   the NMR relaxation data are not fitted well even for
                   quite modest anisotropies (r = 1.3). The extended
                   model-free formula yields an improved fit to the NMR
                   data, but predicts substantial amplitudes of
                   nonexistent slow internal motions (tau approximately
                   greater than 0.2 ns) for many of the nuclei for all r >
                   or = 1.3. The simple model-free formula with the
                   alternate protocol yields even better internal motion
                   parameters than the standard protocol and also an
                   excellent fit to the NMR relaxation data. The best-fit
                   global correlation time for each nucleus corresponds
                   very closely to the theoretical correlation time
                   defined herein. Knowledge of these times would allow
                   one not only to estimate the anisotropy of diffusion
                   but also in favorable cases to infer the existence of
                   slow internal motions. Inclusion of typical statistical
                   errors in R1, R2, and NOE, or modest exchange
                   contributions to R2, seriously degrades the performance
                   of the simple model-free formula with either protocol,
                   especially in regard to the internal relaxation times,
                   which can exhibit very large deviations from their
                   input value even for spherical diffusors. When the
                   fraction of monomers existing as dimers lies in the
                   range 0.1 < or = fd < or = 0.8, none of the three
                   model-free approaches tested yields reliable internal
                   motion parameters.},
  authoraddress  = {Department of Chemistry, University of Washington,
                   Seattle 98195.},
  keywords       = {Algorithms ; Artifacts ; Computer Simulation ;
                   Diffusion ; Hydrogen ; Magnetic Resonance
                   Spectroscopy/*methods ; Models, Chemical ; Molecular
                   Structure ; Nitrogen Isotopes ; Research Support, U.S.
                   Gov't, P.H.S. ; Rotation},
  language       = {eng},
  medline-da     = {19950314},
  medline-dcom   = {19950314},
  medline-edat   = {1994/11/01},
  medline-fau    = {Schurr, J M ; Babcock, H P ; Fujimoto, B S},
  medline-gr     = {P01-GM32681/GM/NIGMS},
  medline-is     = {1064-1866},
  medline-jid    = {9309764},
  medline-lr     = {20041117},
  medline-mhda   = {1994/11/01 00:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {7850167},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Nitrogen Isotopes) ; 1333-74-0 (Hydrogen)},
  medline-sb     = {IM},
  medline-so     = {J Magn Reson B 1994 Nov;105(3):211-24.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=7850167},
  doi            = {10.1006/jmrb.1994.1127},
  year           = 1994
}

@Article{Schwarz78,
  Author         = {Schwarz, G.},
  Title          = {Estimating dimension of a model},
  Journal        = anstat,
  Volume         = {6},
  Number         = {2},
  Pages          = {461-464},
  address        = {IMS Business Office-Suite 6 3401 Investment Blvd,
                   Hayward, CA 94545},
  citedref       = {Akaike H, 1974, IEEE T Automatic Con, V19, P716 ;
                   Schwarz G, 1969, Ann Math Statist, V40, P313 ; Schwarz
                   G, 1971, Ann Math Stat, V42, P1003 ; Tong H, 1975, J
                   Appl Probab, V12, P488},
  isifile-dt     = {Note},
  isifile-ga     = {EQ633},
  isifile-j9     = {Ann Statist},
  isifile-ji     = {Ann. Stat.},
  isifile-nr     = {4},
  isifile-pi     = {Hayward},
  isifile-rp     = {Schwarz, G, Hebrew Univ Jerusalem,Dept Stat,Jerusalem
                   91000,Israel.},
  isifile-sc     = {Statistics \& Probability},
  isifile-tc     = {2886},
  issn           = {0090-5364},
  language       = {English},
  publisher      = {Inst Mathematical Statistics},
  size           = {4 p.},
  sourceid       = {ISI:A1978EQ63300014},
  doi            = {10.1214/aos/1176344136},
  year           = 1978
}

@Article{Shanno70,
  Author         = {Shanno, D. F.},
  Title          = {Conditioning of quasi-{N}ewton methods for function
                   minimization},
  Journal        = mc,
  Volume         = {24},
  Number         = {111},
  Pages          = {647-656},
  address        = {201 CHARLES ST, PROVIDENCE, RI 02940-2213},
  citedref       = {BARNES J, 1965, COMPUT J, V8, P66 ; BOX MJ, 1966,
                   COMPUT J, V9, P67 ; BROYDEN CG, 1965, MATH COMPUT, V19,
                   P577 ; BROYDEN CG, 1967, MATH COMPUT, V21, P368 ;
                   DAVIDON WC, 1959, ANL5990 REP ; FLETCHER R, 1963,
                   COMPUT J, V6, P163 ; GOLDFARB D, 1970, MATH COMPUT,
                   V24, P23 ; LEON A, 1964, COMPARISON AMONG 8 K ; PEARSON
                   JD, 1968, RACTP302 RES AN CORP ; ROSEN EM, 1966, 21ST P
                   NAT M ASS COM, P37 ; SHANNO DF, 1970, MATH COMPUT, V24,
                   P657 ; ZELEZNIK FJ, 1968, J ASSOCIATION COMPUT, V15,
                   P265},
  isifile-dt     = {Article},
  isifile-ga     = {I8761},
  isifile-j9     = {MATH COMPUT},
  isifile-nr     = {12},
  isifile-pi     = {PROVIDENCE},
  isifile-sc     = {Mathematics, Applied},
  isifile-tc     = {548},
  issn           = {0025-5718},
  language       = {English},
  publisher      = {AMER MATHEMATICAL SOC},
  size           = {0 p.},
  sourceid       = {ISI:A1970I876100016},
  doi            = {10.1090/s0025-5718-1970-0274029-x},
  year           = 1970
}

@Article{Smith02,
  Author         = {Smith, P. C. and Firestein, S. and Hunt, J. F.},
  Title          = {The crystal structure of the olfactory marker protein
                   at 2.3 {A} resolution.},
  Journal        = jmb,
  Volume         = {319},
  Number         = {3},
  Pages          = {807-821},
  abstract       = {Olfactory marker protein (OMP) is a highly expressed
                   and phylogenetically conserved cytoplasmic protein of
                   unknown function found almost exclusively in mature
                   olfactory sensory neurons. Electrophysiological studies
                   of olfactory epithelia in OMP knock-out mice show
                   strongly retarded recovery following odorant
                   stimulation leading to an impaired response to pulsed
                   odor stimulation. Although these studies show that OMP
                   is a modulator of the olfactory signal-transduction
                   cascade, its biochemical role is not established. In
                   order to facilitate further studies on the molecular
                   function of OMP, its crystal structure has been
                   determined at 2.3 A resolution using multiwavelength
                   anomalous diffraction experiments on selenium-labeled
                   protein. OMP is observed to form a modified
                   beta-clamshell structure with eight antiparallel
                   beta-strands. While OMP has no significant sequence
                   homology to proteins of known structure, it has a
                   similar fold to a domain found in a variety of existing
                   structures, including in a large family of viral capsid
                   proteins. The surface of OMP is mostly convex and
                   lacking obvious small molecule binding sites,
                   suggesting that it is more likely to be involved in
                   modulating protein-protein interaction than in
                   interacting with small molecule ligands. Three highly
                   conserved regions have been identified as leading
                   candidates for protein-protein interaction sites in
                   OMP. One of these sites represents a loop known to
                   mediate ligand interactions in the structurally
                   homologous EphB2 receptor ligand-binding domain. This
                   site is partially buried in the crystal structure but
                   fully exposed in the NMR solution structure of OMP due
                   to a change in the orientation of an alpha-helix that
                   projects outward from the structurally invariant
                   beta-clamshell core. Gating of this conformational
                   change by molecular interactions in the
                   signal-transduction cascade could be used to control
                   access to OMP's equivalent of the EphB2
                   ligand-interaction loop, thereby allowing OMP to
                   function as a molecular switch.},
  authoraddress  = {Department of Biological Sciences, 702A Fairchild
                   Center, MC 2434, Columbia University, New York, NY
                   10027, USA},
  keywords       = {Amino Acid Sequence ; Animals ; Binding Sites ;
                   Conserved Sequence ; Crystallography, X-Ray ;
                   Electrostatics ; Ligands ; Mice ; Models, Molecular ;
                   Molecular Sequence Data ; Nerve Tissue
                   Proteins/*chemistry/metabolism ; Nuclear Magnetic
                   Resonance, Biomolecular ; Olfactory Marker Protein ;
                   Protein Binding ; Protein Structure, Secondary ;
                   Protein Structure, Tertiary ; Rats ; Receptor
                   Protein-Tyrosine Kinases/chemistry/metabolism ;
                   Receptor, EphB2 ; Research Support, Non-U.S. Gov't ;
                   Research Support, U.S. Gov't, P.H.S. ;
                   Selenium/metabolism ; Signal Transduction},
  language       = {eng},
  doi            = {10.1016/s0022-2836(02)00242-5},
  medline-aid    = {10.1016/S0022-2836(02)00242-5 [doi] ;
                   S0022-2836(02)00242-5 [pii]},
  medline-ci     = {(c) 2002 Elsevier Science Ltd.},
  medline-da     = {20020610},
  medline-dcom   = {20020710},
  medline-edat   = {2002/06/11 10:00},
  medline-fau    = {Smith, Paul C ; Firestein, Stuart ; Hunt, John F},
  medline-is     = {0022-2836 (Print)},
  medline-jid    = {2985088R},
  medline-jt     = {Journal of molecular biology.},
  medline-lr     = {20051117},
  medline-mhda   = {2002/07/12 10:01},
  medline-own    = {NLM},
  medline-pl     = {England},
  medline-pmid   = {12054872},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Ligands) ; 0 (Nerve Tissue Proteins) ; 0 (Olfactory
                   Marker Protein) ; 0 (Omp protein, mouse) ; 0 (Omp
                   protein, rat) ; 7782-49-2 (Selenium) ; EC 2.7.1.112
                   (Receptor Protein-Tyrosine Kinases) ; EC 2.7.1.112
                   (Receptor, EphB2)},
  medline-sb     = {IM},
  medline-si     = {PDB/1F35 ; PDB/1JOB ; PDB/1JOD},
  medline-so     = {J Mol Biol. 2002 Jun 7;319(3):807-21.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=12054872},
  year           = 2002
}

@Article{Steihaug83,
  Author         = {Steihaug, T.},
  Title          = {The conjugate gradient method and trust regions in
                   large scale optimization},
  Journal        = siamjna,
  Volume         = {20},
  Number         = {3},
  Pages          = {626-637},
  address        = {3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA
                   19104-2688},
  citedref       = {AXELLSON O, 1976, LECT NOTES MATH, V572, P1 ; CHANDRA
                   R, 1978, 129 YAL U DEP COMP S ; DENNIS JE, 1979, J
                   OPTIM THEORY APPL, V28, P453 ; EISENSTAT SC, 1982,
                   TR827 RIC U DEP MATH ; ENRIGHT W, 1978, BIT, V18, P276
                   ; GAY DM, 1981, SIAM J SCI STAT COMP, V2, P186 ; HEBDEN
                   MD, 1973, AERE TP515 THEOR PHY ; HESTENES MR, 1952, J
                   RES NBS, V49, P409 ; MORE JJ, 1978, LECT NOTES MATH,
                   V630, P105 ; POWELL MJD, 1970, AERER6469 MATH BRANC ;
                   POWELL MJD, 1970, NONLINEAR PROGRAMMIN, P31 ; POWELL
                   MJD, 1975, NONLINEAR PROGRAMMIN, V2, P1 ; STEIHAUG T,
                   1980, 49 YAL U SCH ORG MAN ; STEIHAUG T, 1982, TR824
                   RIC U DEP MATH ; THOMAS SW, 1975, TR75227 CORN U DEP C
                   ; TOINT PL, 1979, SIAM J NUMER ANAL, V16, P1036},
  isifile-dt     = {Article},
  isifile-ga     = {QU017},
  isifile-j9     = {SIAM J NUMER ANAL},
  isifile-nr     = {16},
  isifile-pi     = {PHILADELPHIA},
  isifile-rp     = {STEIHAUG, T, RICE UNIV,DEPT MATH SCI,HOUSTON,TX 77001.},
  isifile-sc     = {Mathematics, Applied},
  isifile-tc     = {99},
  issn           = {0036-1429},
  language       = {English},
  publisher      = {SIAM PUBLICATIONS},
  size           = {12 p.},
  sourceid       = {ISI:A1983QU01700012},
  doi            = {10.1137/0720042},
  year           = 1983
}

@Article{Stone92,
  Author         = {Stone, M. J. and Fairbrother, W. J. and Palmer, A. G.
                   and Reizer, J. and Saier, M. H. and Wright, P. E.},
  Title          = {Backbone dynamics of the {\em{B}acillus subtilis}
                   glucose permease-{IIA} domain determined from {N}-15
                   {NMR} relaxation measurements},
  Journal        = biochem,
  Volume         = {31},
  Number         = {18},
  Pages          = {4394-4406},
  abstract       = {The backbone dynamics of the uniformly N-15-labeled
                   IIA domain of the glucose permease of Bacillus subtilis
                   have been characterized using inverse-detected
                   two-dimensional H-1-N-15 NMR spectroscopy. Longitudinal
                   (T1) and transverse (T2) N-15 relaxation time constants
                   and steady-state \{H-1\}-N-15 NOEs were measured, at a
                   spectrometer proton frequency of 500 MHz, for 137
                   (91\%) of the 151 protonated backbone nitrogens. These
                   data were analyzed by using a model-free dynamics
                   formalism to determine the generalized order parameter
                   (S2), the effective correlation time for internal
                   motions (tau(e)), and N-15 exchange broadening
                   contributions (R(ex)) for each residue, as well as the
                   overall molecular rotational correlation time (tau(m)).
                   The T1 and T2 values for most residues were in the
                   ranges 0.45-0.55 and 0.11-0.15 s, respectively;
                   however, a small number of residues exhibited
                   significantly slower relaxation. Similarly,
                   \{H-1\}-N-15 NOE values for most residues were in the
                   range 0.72-0.80, but a few residues had much smaller
                   positive NOEs and some exhibited negative NOEs. The
                   molecular rotational correlation time was 6.24 +/- 0.01
                   ns; most residues had order parameters in the range
                   0.75-0.90 and tau(e) values of less than ca. 25 ps.
                   Residues found to be more mobile than the average were
                   concentrated in three areas: the N-terminal residues
                   (1-13), which were observed to be highly disordered;
                   the loop from P25 to D41, the apex of which is situated
                   adjacent to the active site and may have a role in
                   binding to other proteins; and the region from A146 to
                   S149. All mobile residues occurred in regions close to
                   termini, in loops, or in irregular secondary structure.},
  address        = {1155 16TH ST, NW, Washington, DC 20036},
  authoraddress  = {Scripps Res Inst, Dept Molec Biol, LA Jolla, CA 92037
                   USA. ; Univ Calif San Diego, Dept Biol, LA Jolla, CA
                   92093 USA.},
  citedref       = {ABRAGAM A, 1961, PRINCIPLES NUCL MAGN, P264 ; ALGER
                   JR, 1984, Q REV BIOPHYS, V17, P83 ; BENNETT WS, 1983,
                   CRC CRIT REV BIOCH, V15, P290 ; BLOOM M, 1965, J CHEM
                   PHYS, V42, P1615 ; BOYD J, 1990, CHEM PHYS LETT, V175,
                   P477 ; BURUM DP, 1980, J MAGN RESON, V39, P163 ; CARR
                   HY, 1954, PHYS REV, V94, P630 ; CLORE GM, 1990,
                   BIOCHEMISTRY-US, V29, P7387 ; CLORE GM, 1990, J AM CHEM
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                   P21005 ; DEBOER M, 1986, J BACTERIOL, V167, P393 ;
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                   1969, BIOPOLYMERS, V7, P379 ; ENGLANDER SW, 1984, Q REV
                   BIOPHYS, V16, P521 ; FAIRBROTHER WJ, 1991,
                   BIOCHEMISTRY-US, V30, P6896 ; FAIRBROTHER WJ, 1992,
                   BIOCHEMISTRY-US, V31, P4413 ; FAIRBROTHER WJ, 1992,
                   FEBS LETT, V296, P148 ; FEDOTOV VD, 1987, J BIOMOL
                   STRUCT DYN, V4, P599 ; GURD FRN, 1979, ADV PROTEIN
                   CHEM, V33, P73 ; HIYAMA Y, 1988, J AM CHEM SOC, V110,
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                   1989, BIOCHEMISTRY-US, V28, P8972 ; KAY LE, 1992, IN
                   PRESS J MAGN RESO ; KRAULIS PJ, 1991, J APPL
                   CRYSTALLOGR, V24, P945 ; LED JJ, 1989, METHOD ENZYMOL,
                   V176, P311 ; LIAO DI, 1991, BIOCHEMISTRY-US, V30, P9583
                   ; LIPARI G, 1982, J AM CHEM SOC, V104, P4546 ; LIPARI
                   G, 1982, J AM CHEM SOC, V104, P4559 ; LONDON RE, 1980,
                   MAGNETIC RESONANCE B, P1 ; MAGASANIK B, 1970, LACTOSE
                   OPERON, P189 ; MARION D, 1983, BIOCHEM BIOPH RES CO,
                   V113, P967 ; MARION D, 1989, J MAGN RESON, V84, P425 ;
                   MEADOW ND, 1990, ANNU REV BIOCHEM, V59, P497 ; MEIBOOM
                   S, 1958, REV SCI INSTRUM, V29, P688 ; MESSERLE BA,
                   1989, J MAGN RESON, V85, P608 ; MOLDAY RS, 1972,
                   BIOCHEMISTRY-US, V11, P150 ; MORRIS GA, 1979, J AM CHEM
                   SOC, V101, P760 ; NELSON SO, 1983, EMBO J, V2, P715 ;
                   NIRMALA NR, 1988, J AM CHEM SOC, V110, P7557 ; NIRMALA
                   NR, 1989, J MAGN RESON, V82, P659 ; NOVOTNY MJ, 1985, J
                   BACTERIOL, V162, P810 ; OSUMI T, 1982, P NATL ACAD SCI
                   USA, V79, P1457 ; PALMER AG, 1991, J AM CHEM SOC, V113,
                   P4371 ; PALMER AG, 1991, J MAGN RESON, V93, P151 ;
                   PALMER AG, 1992, MOL PHYS, V75, P699 ; POSTMA PW, 1984,
                   J BACTERIOL, V158, P351 ; PRESS WH, 1986, NUMERICAL
                   RECIPES ; RAO BDN, 1989, METHOD ENZYMOL, V176, P279 ;
                   RATKOWSKY DA, 1983, NONLINEAR REGRESSION ; REIZER J,
                   1988, CRC CRIT R MICROBIOL, V15, P297 ; REIZER J, 1991,
                   IN PRESS J BIOL CHEM ; RINGE D, 1985, PROG BIOPHYS MOL
                   BIO, V45, P197 ; RODER H, 1989, METHOD ENZYMOL, V176,
                   P446 ; SAIER MH, 1983, J BACTERIOL, V155, P1351 ; SAIER
                   MH, 1989, MICROBIOL REV, V53, P109 ; SHAKA AJ, 1985, J
                   MAGN RESON, V64, P547 ; SHOJI A, 1989, MACROMOLECULES,
                   V22, P2860 ; SHOJI A, 1990, J AM CHEM SOC, V112, P4693
                   ; SMITH GM, 1987, BIOCHEMISTRY-US, V26, P2202 ; SUTRINA
                   SL, 1990, J BIOL CHEM, V265, P18581 ; VOLD RR, 1976, J
                   CHEM PHYS, V64, P320 ; WAGNER G, 1983, Q REV BIOPHYS,
                   V16, P1 ; WELCH GR, 1982, PROG BIOPHYS MOL BIO, V39,
                   P109 ; WILLIAMS RJP, 1979, BIOL REV, V54, P389 ;
                   WILLIAMS RJP, 1989, EUR J BIOCHEM, V183, P479 ; WOOTTON
                   JC, 1989, PROTEIN ENG, V2, P535 ; WRIGHT LL, 1988,
                   BIOPHYS J, V54, P463 ; WUTHRICH K, 1986, NMR PROTEINS
                   NUCL AC, P24 ; ZANG LH, 1990, BIOCHEMISTRY-US, V29,
                   P6815},
  isifile-dt     = {Article},
  isifile-ga     = {HU223},
  isifile-j9     = {Biochemistry-USA},
  isifile-ji     = {Biochemistry},
  isifile-nr     = {70},
  isifile-pi     = {Washington},
  isifile-sc     = {Biochemistry \& Molecular Biology},
  isifile-tc     = {186},
  issn           = {0006-2960},
  keywords       = {[ISI:] sugar phosphotransferase system; nuclear
                   magnetic-resonance; model-free approach; chemical-shift
                   tensors; escherichia-coli; salmonella-typhimurium;
                   inducer exclusion; hydrogen-exchange; glycerol kinase;
                   enzyme-iiiglc ;;},
  language       = {English},
  month          = {May 12},
  publisher      = {Amer Chemical Soc},
  size           = {13 p.},
  sourceid       = {ISI:A1992HU22300003},
  year           = 1992
}

@Article{Sugase13,
  Author         = {Sugase, K. and Konuma, T. and Lansing, J. C. and
                   Wright, P. E.},
  Title          = {Fast and accurate fitting of relaxation dispersion
                   data using the flexible software package {GLOVE}.},
  Journal        = jbnmr,
  Volume         = {56},
  Number         = {3},
  Pages          = {275-283},
  abstract       = {Relaxation dispersion spectroscopy is one of the most
                   widely used techniques for the analysis of protein
                   dynamics. To obtain a detailed understanding of the
                   protein function from the view point of dynamics, it is
                   essential to fit relaxation dispersion data accurately.
                   The grid search method is commonly used for relaxation
                   dispersion curve fits, but it does not always find the
                   global minimum that provides the best-fit parameter
                   set. Also, the fitting quality does not always improve
                   with increase of the grid size although the
                   computational time becomes longer. This is because
                   relaxation dispersion curve fitting suffers from a
                   local minimum problem, which is a general problem in
                   non-linear least squares curve fitting. Therefore, in
                   order to fit relaxation dispersion data rapidly and
                   accurately, we developed a new fitting program called
                   GLOVE that minimizes global and local parameters
                   alternately, and incorporates a Monte-Carlo
                   minimization method that enables fitting parameters to
                   pass through local minima with low computational cost.
                   GLOVE also implements a random search method, which
                   sets up initial parameter values randomly within
                   user-defined ranges. We demonstrate here that the
                   combined use of the three methods can find the global
                   minimum more rapidly and more accurately than grid
                   search alone.},
  authoraddress  = {Bioorganic Research Institute, Suntory Foundation for
                   Life Sciences, 1-1-1 Wakayamadai Shimamoto, Mishima,
                   Osaka, 618-8503, Japan.},
  language       = {eng},
  medline-aid    = {10.1007/s10858-013-9747-5 [doi]},
  medline-crdt   = {2013/06/12 06:00},
  medline-da     = {20130703},
  medline-dep    = {20130611},
  medline-edat   = {2013/06/12 06:00},
  medline-fau    = {Sugase, Kenji ; Konuma, Tsuyoshi ; Lansing, Jonathan C
                   ; Wright, Peter E},
  medline-gr     = {R01 GM075995/GM/NIGMS NIH HHS/United States},
  medline-is     = {1573-5001 (Electronic) ; 0925-2738 (Linking)},
  medline-jid    = {9110829},
  medline-jt     = {Journal of biomolecular NMR},
  medline-lid    = {10.1007/s10858-013-9747-5 [doi]},
  medline-mhda   = {2013/06/12 06:00},
  medline-own    = {NLM},
  medline-phst   = {2013/01/29 [received] ; 2013/05/21 [accepted] ;
                   2013/06/11 [aheadofprint]},
  medline-pl     = {Netherlands},
  medline-pmid   = {23754491},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR. 2013 Jul;56(3):275-83. doi:
                   10.1007/s10858-013-9747-5. Epub 2013 Jun 11.},
  medline-stat   = {In-Data-Review},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=23754491},
  doi            = {10.1007/s10858-013-9747-5},
  year           = 2013
}

@Article{Sun11,
  Author = {Sun, H. and d'Auvergne, E. J. and Reinscheid, U. M. and Dias, L. C. and Andrade, C. K. Z. and Rocha, Rafael O. and Griesinger, C.},
  Title = {Bijvoet in Solution Reveals Unexpected Stereoselectivity in a Michael Addition},
  Journal = cej,
  Year = {2011},
  Volume = {17},
  Number = {6},
  Pages = {1811-1817},
  Abstract = {The absolute configuration of small crystallizable molecules can be
     determined with anomalous X-ray diffraction as shown by Bijvoet in 1951.
     For the majority of compounds that can neither be crystallized nor
     easily be converted into crystallizable derivatives, stereocontrolled
     organic synthesis is still required to establish their absolute
     configuration. In this contribution, a new fundamental methodology for
     resolving the absolute configuration will be presented that does not
     require crystallization. With residual dipolar coupling enhanced NMR
     spectroscopy, ensembles of a limited number of structures are created
     reflecting the correct conformations and relative configuration.
     Subsequently, from these ensembles, optical rotation dispersion},
  Publisher = {WILEY-BLACKWELL},
  Address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA},
  Type = {Article},
  Language = {English},
  Affiliation = {Reinscheid, UM (Reprint Author), Max Planck Inst Biophys Chem, Dept NMR Based Struct Biol, Fassberg 11, D-37077 Gottingen, Germany.
     Sun, Han; d'Auvergne, Edward J.; Reinscheid, Uwe M.; Griesinger, Christian, Max Planck Inst Biophys Chem, Dept NMR Based Struct Biol, D-37077 Gottingen, Germany.
     Dias, Luiz Carlos, Univ Estadual Campinas, Inst Quim, Lab Sintese Organ, BR-13084971 Campinas, SP, Brazil.
     Andrade, Carlos Kleber Z.; Rocha, Rafael Oliveira, Univ Brasilia, Inst Quim, Lab Quim Metodol \& Organ Sintet, BR-70904970 Brasilia, DF, Brazil.},
  DOI = {10.1002/chem.201002520},
  ISSN = {0947-6539},
  Keywords = {configuration determination; Michael addition; niobium; NMR
     spectroscopy; optical rotation dispersion},
  Keywords-Plus = {DENSITY-FUNCTIONAL THEORY; CONSISTENT FORCE-FIELD;
     ALPHA,BETA-UNSATURATED KETONES; ORGANIC-SYNTHESIS; OPTICAL-ROTATION;
     ENHANCED NMR; MODEL-FREE; STEREOCHEMISTRY; CONFIGURATION; OPTIMIZATION},
  Subject-Category = {Chemistry},
  Web-of-Science-Category = {Chemistry, Multidisciplinary},
  Author-Email = {urei@nmr.mpibpc.mpg.de
     ldias@iqm.unicamp.br
     ckleber@unb.br
     rafaelrocha@unb.br
     cigr@nmr.mpibpc.mpg.de},
  Funding-Acknowledgement = {IQ-UnB; IQ-UNICAMP; CAPES; CNPq; FINATEC; CT-Infra\{{[}\}0970/01]; Max
     Planck Society; Deutsche Forschungsgemeinschaft\{{[}\}GRK 782, FOR 934];
     Fonds der Chemischen Industrie},
  Funding-Text = {R.O.R.. C.K.Z.A., and L.C.D. thank IQ-UnB, IQ-UNICAMP, CAPES, CNPq,
     FINATEC, CT-Infra 0970/01 and C.G. thanks the Max Planck Society, the
     Deutsche Forschungsgemeinschaft (GRK 782 and FOR 934) and the Fonds der
     Chemischen Industrie for financial support. The authors thank Prof.
     Michael Reggelin for the ORD measurement and Dr. Burkhard Luy for
     providing the PAN gel.},
  Number-of-Cited-References = {38},
  Times-Cited = {3},
  Journal-ISO = {Chem.-Eur. J.},
  Doc-Delivery-Number = {727GW},
  Unique-ID = {ISI:000287787100012},
}

@Article{Tjandra95b,
  Author         = {Tjandra, N. and Feller, S. E. and Pastor, R. W. and
                   Bax, A.},
  Title          = {Rotational diffusion anisotropy of human ubiquitin
                   from {N}-15 {NMR} relaxation},
  Journal        = jacs,
  Volume         = {117},
  Number         = {50},
  Pages          = {12562-12566},
  abstract       = {. Longitudinal and transverse N-15 NMR relaxation
                   times in human ubiquitin have been measured at 600-MHz
                   H-1 frequency with a reproducibility of better than
                   1\%. Two independent measurements of the N-15-\{H-1\}
                   NOE indicate a random error of ca. 0.01, and no values
                   were larger than the theoretical maximum. The
                   relaxation data are incompatible with isotropic
                   rotational diffusion but agree well with an axially
                   symmetric rotational diffusion tensor with a diffusion
                   anisotropy, D-parallel to/D-perpendicular to Of 1.17
                   There is no statistically significant further
                   improvement in the fit between the experimental data
                   and those predicted by a fully asymmetric diffusion
                   tensor, confirming that the rotational diffusion tensor
                   of ubiquitin is axially symmetric within experimental
                   uncertainty. The relative ratio of the principal
                   components of the inertia tensor calculated from the
                   X-ray structure is 1.00:0.90:0.64, and the axis with
                   the smallest inertia component makes an angle of 11
                   degrees with the unique axis of the experimentally
                   determined diffusion tenser. Hydrodynamic calculations
                   agree well with experimental results, provided half a
                   shell of bound water is included and flexibility of the
                   C-terminal residues is accounted for either by omitting
                   them from the calculations or by using conformations
                   for these residues obtained from a Langevin dynamics
                   simulation.},
  address        = {1155 16TH ST, NW, WASHINGTON, DC 20036},
  authoraddress  = {NIDDKD,CHEM PHYS LAB,BETHESDA,MD 20892. ; US FDA,CTR
                   BIOL EVALUAT \& RES,BIOPHYS LAB,BETHESDA,MD 20892.},
  citedref       = {BARBATO G, 1992, BIOCHEMISTRY-US, V31, P5269 ;
                   BEVINGTON PR, 1992, DATA REDUCTION ERROR, P205 ; BRAATZ
                   JA, 1992, J BIOMOL STRUCT DYN, V9, P935 ; BROOKS BR,
                   1983, J COMPUT CHEM, V4, P187 ; BRUSCHWEILER R, 1995,
                   SCIENCE, V268, P886 ; CLORE GM, 1990, J AM CHEM SOC,
                   V112, P4989 ; DELAGLIO F, 1995, IN PRESS J BIOMOL NM ;
                   DELATORRE JG, 1981, Q REV BIOPHYS, V14, P81 ; DELLWO
                   MJ, 1989, J AM CHEM SOC, V111, P4571 ; FARROW NA, 1995,
                   J BIOMOL NMR, V6, P153 ; GARRETT DS, 1991, J MAGN
                   RESON, V95, P214 ; GRZESIEK S, 1993, J AM CHEM SOC,
                   V115, P12593 ; HAGERMAN PJ, 1981, BIOPOLYMERS, V20,
                   P1481 ; ISHIMA R, 1995, J BIOMOL NMR, V6, P217 ; KAY
                   LE, 1987, J MAGN RESON, V73, P558 ; KAY LE, 1989,
                   BIOCHEMISTRY-US, V28, P8972 ; KAY LE, 1992, J MAGN
                   RESON, V97, P359 ; LIPARI G, 1982, J AM CHEM SOC, V104,
                   P4546 ; LIPARI G, 1982, J AM CHEM SOC, V104, P4559 ;
                   LONCHARICH RJ, 1992, BIOPOLYMERS, V32, P523 ; MACKERELL
                   AD, 1992, FASEB J, V6, A143 ; NIRMALA NR, 1988, J AM
                   CHEM SOC, V110, P7557 ; NIRMALA NR, 1989, J MAGN RESON,
                   V82, P659 ; PALMER AG, 1992, MOL PHYS, V75, P699 ; PENG
                   JW, 1992, BIOCHEMISTRY-US, V31, P8571 ; PENG JW, 1992,
                   J MAGN RESON, V98, P308 ; SCHNEIDER DM, 1992,
                   BIOCHEMISTRY-US, V31, P3645 ; SCHURR JM, 1994, J MAGN
                   RESON SER B, V105, P211 ; SKLENAR V, 1987, J MAGN
                   RESON, V73, P375 ; TJANDRA N, 1995, EUR J BIOCHEM,
                   V230, P1014 ; VENABLE RM, 1988, BIOPOLYMERS, V27, P1001
                   ; VIJAYKUMAR S, 1987, J MOL BIOL, V194, P531 ; WANG AC,
                   1995, J BIOMOL NMR, V5, P376 ; WOESSNER DE, 1962, J
                   CHEM PHYS, V37, P647},
  isifile-dt     = {Article},
  isifile-ga     = {TL733},
  isifile-j9     = {J Amer Chem Soc},
  isifile-ji     = {J. Am. Chem. Soc.},
  isifile-nr     = {34},
  isifile-pi     = {Washington},
  isifile-sc     = {Chemistry, Multidisciplinary},
  isifile-tc     = {337},
  issn           = {0002-7863},
  keywords       = {[ISI:] model-free approach; magnetic-resonance
                   relaxation; correlation spectroscopy; backbone
                   dynamics; cross-correlation; proteins; macromolecules;
                   simulations; dipolar; times ;;},
  language       = {English},
  month          = {Dec 20},
  publisher      = {Amer CHemical Soc},
  size           = {5 p.},
  sourceid       = {ISI:A1995TL73300020},
  year           = 1995
}

@Article{Tjandra95a,
  Author         = {Tjandra, N. and Kuboniwa, H. and Ren, H. and Bax, A.},
  Title          = {Rotational dynamics of calcium-free calmodulin studied
                   by 15{N}-{NMR} relaxation measurements.},
  Journal        = ejb,
  Volume         = {230},
  Number         = {3},
  Pages          = {1014-1024},
  abstract       = {The backbone motions of calcium-free Xenopus
                   calmodulin have been characterized by measurements of
                   the 15N longitudinal relaxation times (T1) at 51 and 61
                   MHz, and by conducting transverse relaxation (T2),
                   spin-locked transverse relaxation (T1 rho), and
                   15N-[1H] heteronuclear NOE measurements at 61 MHz 15N
                   frequency. Although backbone amide hydrogen exchange
                   experiments indicate that the N-terminal domain is more
                   stable than calmodulin's C-terminal half, slowly
                   exchanging backbone amide protons are found in all
                   eight alpha-helices and in three of the four short
                   beta-strands. This confirms that the calcium-free form
                   consists of stable secondary structure and does not
                   adopt a 'molten globule' type of structure. However,
                   the C-terminal domain of calmodulin is subject to
                   conformational exchange on a time scale of about 350
                   microseconds, which affects many of the C-terminal
                   domain residues. This results in significant shortening
                   of the 15N T2 values relative to T1 rho, whereas the T1
                   rho and T2 values are of similar magnitude in the
                   N-terminal half of the protein. A model in which the
                   motion of the protein is assumed to be isotropic
                   suggests a rotational correlation time for the protein
                   of about 8 ns but quantitatively does not agree with
                   the magnetic field dependence of the T1 values and does
                   not explain the different T2 values found for different
                   alpha-helices in the N-terminal domain. These latter
                   parameters are compatible with a flexible dumb-bell
                   model in which each of calmodulin's two domains freely
                   diffuse in a cone with a semi-angle of about 30 degrees
                   and a time constant of about 3 ns, whereas the overall
                   rotation of the protein occurs on a much slower time
                   scale of about 12 ns. The difference in the transverse
                   relaxation rates observed between the amides in helices
                   C and D suggests that the change in interhelical angle
                   upon calcium binding is less than predicted by Herzberg
                   et al. Strynadka and James [Strynadka, N. C. J. \&
                   James, M. N. G. (1988) Proteins Struct. Funct. Genet.
                   3, 1-17].},
  authoraddress  = {Laboratory of Chemical Physics, National Institute of
                   Diabetes and Digestive and Kidney Diseases, National
                   Institutes of Health, Bethesda, MD 20892-0520, USA.},
  keywords       = {Animals ; Anisotropy ; Calcium/analysis ;
                   Calmodulin/*chemistry ; Magnetic Resonance Spectroscopy
                   ; Protein Conformation ; Recombinant Proteins/chemistry
                   ; Research Support, U.S. Gov't, P.H.S. ; Rotation ;
                   Xenopus},
  language       = {eng},
  medline-da     = {19950810},
  medline-dcom   = {19950810},
  medline-edat   = {1995/06/15},
  medline-fau    = {Tjandra, N ; Kuboniwa, H ; Ren, H ; Bax, A},
  medline-gr     = {1F32DK09143-01/DK/NIDDK},
  medline-is     = {0014-2956},
  medline-jid    = {0107600},
  medline-lr     = {20041117},
  medline-mhda   = {1995/06/15 00:01},
  medline-own    = {NLM},
  medline-pl     = {GERMANY},
  medline-pmid   = {7601131},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Calmodulin) ; 0 (Recombinant Proteins) ; 7440-70-2
                   (Calcium)},
  medline-sb     = {IM},
  medline-so     = {Eur J Biochem 1995 Jun 15;230(3):1014-24.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=7601131},
  year           = 1995
}

@Article{Tjandra96,
  Author         = {Tjandra, N. and Wingfield, P. and Stahl, S. and Bax,
                   A.},
  Title          = {Anisotropic rotational diffusion of perdeuterated
                   {HIV} protease from {N}-15 {NMR} relaxation
                   measurements at two magnetic},
  Journal        = jbnmr,
  Volume         = {8},
  Number         = {3},
  Pages          = {273-284},
  abstract       = {N-15 NMR relaxation times in perdeuterated HIV-1
                   protease, complexed with the sub-nanomolar inhibitor
                   DMP323, have been measured at 600 and 360 MHz H-1
                   frequency. The relative magnitudes of the principal
                   components of the inertia tensor, calculated from the
                   X-ray coordinates of the protein-drug complex, are
                   1.0:0.85:0.44. The relation between the T-1/T-2 ratios
                   observed for the individual backbone amides and their
                   N-H orientation within the 3D structure of the protease
                   dimer yields a rotational diffusion tensor oriented
                   nearly collinear to the inertia tenser. The relative
                   magnitudes of its principal components (1.00:1.11:1.42)
                   are also in good agreement with hydrodynamic modeling
                   results. The orientation and magnitude of the diffusion
                   tensors derived from relaxation data obtained at 360
                   and 600 MHz are nearly identical. The anisotropic
                   nature of the rotational diffusion has little influence
                   on the order parameters derived from the N-15 T-1 and
                   T-2 relaxation times; however, if anisotropy is
                   ignored, this can result in erroneous identification of
                   either exchange broadening or internal motions on a
                   nanosecond time scale. The average ratio of the T-1
                   values measured at 360 and 600 MHz is 0.50+/-0.015,
                   which is slightly larger than the value of 0.466
                   expected for an isotropic rigid rotor with tau(c)=10.7
                   ns. The average ratio of the T-2 values measured at 360
                   and 600 MHz is 1.14+/-0.04, which is also slightly
                   larger than the expected ratio of 1.11, This magnetic
                   field dependence of the T-1 and T-2 relaxation times
                   suggests that the spectral density contribution from
                   fast internal motions is not negligible, and that the
                   chemical shift anisotropy of peptide backbone amides,
                   on average, is larger than the 160 ppm value commonly
                   used in N-15 relaxation studies of proteins.},
  address        = {PO BOX 214, 2300 AE LEIDEN, NETHERLANDS},
  authoraddress  = {NIAMSD,PROT EXPRESS LAB,NIH,BETHESDA,MD 20892.},
  citedref       = {ALLERHAND A, 1971, J AM CHEM SOC, V93, P544 ; BARBATO
                   G, 1992, BIOCHEMISTRY-US, V31, P5269 ; BEVINGTON PR,
                   1992, DATA REDUCTION ERROR, P205 ; BOYD J, 1990, CHEM
                   PHYS LETT, V175, P477 ; BRUSCHWEILER R, 1995, SCIENCE,
                   V268, P886 ; CLORE GM, 1990, BIOCHEMISTRY-US, V29,
                   P7387 ; CLORE GM, 1990, J AM CHEM SOC, V112, P4989 ;
                   COLE HBR, 1991, CHEM PHYS, V158, P271 ; DAVIS DG, 1994,
                   J MAGN RESON SER B, V104, P266 ; DELATORRE JG, 1981, Q
                   REV BIOPHYS, V14, P81 ; DELLWO MJ, 1989, J AM CHEM SOC,
                   V111, P4571 ; GRZESIEK S, 1993, J AM CHEM SOC, V115,
                   P12593 ; HANSEN AP, 1994, BIOCHEMISTRY-US, V33, P15418
                   ; HIYAMA Y, 1988, J AM CHEM SOC, V110, P2378 ; KAY LE,
                   1989, BIOCHEMISTRY-US, V28, P8972 ; KAY LE, 1992, J
                   MAGN RESON, V97, P359 ; KING R, 1978, BIOPHYS J, V6,
                   P103 ; KORDEL J, 1992, BIOCHEMISTRY-US, V31, P4856 ;
                   LAM PYS, 1994, SCIENCE, V263, P380 ; LIPARI G, 1982, J
                   AM CHEM SOC, V104, P4546 ; LIPARI G, 1982, J AM CHEM
                   SOC, V104, P4559 ; LONDON RE, 1980, MAGNETIC RESONANCE
                   B, P1 ; NICHOLSON LK, 1995, NAT STRUCT BIOL, V2, P274 ;
                   NIRMALA NR, 1988, J AM CHEM SOC, V110, P7557 ; OAS TG,
                   1987, J AM CHEM SOC, V109, P5962 ; PALMER AG, 1993,
                   CURR OPIN BIOTECH, V4, P385 ; PENG JW, 1991, J MAGN
                   RESON, V95, P421 ; PENG JW, 1992, BIOCHEMISTRY-US, V31,
                   P8571 ; PENG JW, 1995, BIOCHEMISTRY-US, V34, P16733 ;
                   PHAN I, 1996, IN PRESS J BIOMOL NM ; SCHNEIDER DM,
                   1992, BIOCHEMISTRY-US, V31, P3645 ; SCHURR JM, 1994, J
                   MAGN RESON SER B, V105, P211 ; TJANDRA N, 1995, EUR J
                   BIOCHEM, V230, P1014 ; TJANDRA N, 1995, J AM CHEM SOC,
                   V117, P12562 ; TJANDRA N, 1996, IN PRESS J AM CHEM S ;
                   TORCHIA DA, 1993, NMR PROTEINS, P190 ; WAGNER G, 1993,
                   CURR OPIN STRUC BIOL, V3, P748 ; WOESSNER DE, 1962, J
                   CHEM PHYS, V37, P647 ; WUTHRICH K, 1978, TRENDS BIOCHEM
                   SCI, V3, P227},
  isifile-dt     = {Article},
  isifile-ga     = {VW192},
  isifile-j9     = {J Biomol NMR},
  isifile-ji     = {J. Biomol. NMR},
  isifile-nr     = {39},
  isifile-pi     = {LEIDEN},
  isifile-rp     = {Tjandra, N, NIDDKD,Chem Phys Lab,NIH,Bldg
                   2,Bethesda,MD 20892.},
  isifile-sc     = {Biochemistry \& Molecular Biology; Spectroscopy},
  isifile-tc     = {143},
  issn           = {0925-2738},
  keywords       = {N-15 NMR; rotational diffusion; chemical shift
                   anisotropy; dynamics; magnetic field dependence;
                   deuteration ; [ISI:] model-free approach; backbone
                   dynamics; staphylococcal nuclease; resonance
                   relaxation; cross-correlation; spectroscopy;
                   macromolecules; proteins; dipolar; range ;;},
  language       = {English},
  month          = {OCT},
  publisher      = {Escom Sci Publ BV},
  size           = {12 p.},
  sourceid       = {ISI:A1996VW19200005},
  doi            = {10.1007/bf00410326},
  year           = 1996
}

@Article{Tollinger01,
  Author         = {Tollinger, M. and Skrynnikov, N. R. and Mulder, F. A. A. and Forman-Kay, J. D. and Kay, L. E.},
  Title          = {Slow Dynamics in Folded and Unfolded States of an SH3 Domain},
  Journal        = jacs,
  Volume         = {123},
  Pages          = {11341-11352},
  Number         = {46},
  abstract       = {15N relaxation dispersion experiments were applied to the isolated
                   N-terminal SH3 domain of the Drosophila protein drk (drkN SH3) to
                   study microsecond to second time scale exchange processes. The drkN
                   SH3 domain exists in equilibrium between folded (Fexch) and unfolded
                   (Uexch) states under nondenaturing conditions in a ratio of 2:1 at
                   20 C, with an average exchange rate constant, kex, of 2.2 s-1 (slow
                   exchange on the NMR chemical shift time scale). Consequently a discrete
                   set of resonances is observed for each state in NMR spectra. Within
                   the Uexch ensemble there is a contiguous stretch of residues undergoing
                   conformational exchange on a μs/ms time scale, likely due to local,
                   non-native hydrophobic collapse. For these residues both the Fexch
                   - Uexch conformational exchange process and the μs/ms exchange
                   event within the Uexch state contribute to the 15N line width and
                   can be analyzed using CPMG-based 15N relaxation dispersion measurements.
                   The contribution of both processes to the apparent relaxation rate
                   can be deconvoluted numerically by combining the experimental 15N
                   relaxation dispersion data with results from an 15N longitudinal
                   relaxation experiment that accurately quantifies exchange rates in
                   slow exchanging systems (Farrow, N. A.; Zhang, O.; Forman-Kay, J.
                   D.; Kay, L. E. J. Biomol. NMR 1994, 4, 727−734). A simple, generally
                   applicable analytical expression for the dependence of the effective
                   transverse relaxation rate constant on the pulse spacing in CPMG
                   experiments has been derived for a two-state exchange process in
                   the slow exchange limit, which can be used to fit the experimental
                   data on the global folding/unfolding transition. The results illustrate
                   that relaxation dispersion experiments provide an extremely sensitive
                   tool to probe conformational exchange processes in unfolded states
                   and to obtain information on the free energy landscape of such systems.},
  doi            = {10.1021/ja011300z},
  eprint         = {http://pubs.acs.org/doi/pdf/10.1021/ja011300z},
  url            = {http://dx.doi.org/10.1021/ja011300z},
  year           = 2001
}

@Article{Trott03,
  Author         = {Trott, O and Abergel, D and Palmer, AG},
  Title          = {An average-magnetization analysis of {R}-1 rho
                   relaxation outside of the fast exchange},
  Journal        = mp,
  Volume         = {101},
  Number         = {6},
  Pages          = {753-763},
  abstract       = {Approximate expressions for the {NMR} spin relaxation
                   rate constant in the rotating frame of reference {R}-1rho
                   are derived for two-site chemical exchange by
                   consideration of the evolution of the average density
                   operator using the stochastic {L}iouville equation.
                   {R}-1rho is obtained as a linearized approximation to the
                   largest (least negative) eigenvalue of the matrix
                   describing the evolution of the average density
                   operator in the long-term limit. The expressions
                   obtained are more accurate than existing expressions
                   when exchange is not fast and the populations of the
                   exchanging sites are close to equal. The new
                   expressions for {R}-1rho facilitate the interpretation of
                   chemical exchange phenomena in proteins and other
                   biological macromolecules.},
  address        = {4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON,
                   ENGLAND},
  affiliation    = {Abergel, D (Reprint Author), Ecole Normale Super,
                   Chim Lab, F-75005 Paris, France. Ecole Normale Super,
                   Chim Lab, F-75005 Paris, France. Columbia Univ, Dept
                   Biochem \& Mol Biophys, New York, NY 10032 USA.},
  doc-delivery-number = {660MA},
  doi            = {10.1080/0026897021000054826},
  issn           = {0026-8976},
  journal-iso    = {Mol. Phys.},
  keywords-plus  = {SPIN},
  language       = {English},
  number-of-cited-references = {19},
  publisher      = {TAYLOR \& FRANCIS LTD},
  research-areas = {Physics},
  times-cited    = {18},
  type           = {Article},
  unique-id      = {ISI:000181835900005},
  web-of-science-categories = {Physics, Atomic, Molecular \& Chemical},
  year           = 2003
}

@Article{TrottPalmer02,
  Author         = {Trott, O. and Palmer, 3rd, A. G.},
  Title          = {R1rho relaxation outside of the fast-exchange limit.},
  Journal        = jmr,
  Volume         = {154},
  Number         = {1},
  Pages          = {157-160},
  abstract       = {Chemical-exchange effects in NMR spectroscopy enable
                   kinetic processes to be characterized at equilibrium in
                   solution. Beginning with the Bloch-McConnell equations,
                   new expressions are derived for the spin relaxation
                   rate constant in the rotating frame, R1rho, for
                   chemical exchange between two sites that have distinct
                   magnetic environments and Larmor frequencies. The
                   results are accurate provided that the spin relaxation
                   decay is dominated by a single exponential damping
                   constant and are applicable to a wider range of
                   conditions than existing theoretical descriptions. The
                   new expressions for R1rho will be particularly useful
                   in analyzing experimental data when exchange is not
                   fast and site populations are unequal.},
  authoraddress  = {Department of Biochemistry and Molecular Biophysics,
                   Columbia University, 630 West 168th Street, New York,
                   New York 10032, USA.},
  keywords       = {*Magnetic Resonance Spectroscopy ; Mathematics ;
                   Models, Theoretical ; Solutions},
  language       = {eng},
  medline-aid    = {10.1006/jmre.2001.2466 [doi] ; S1090780701924668 [pii]},
  medline-crdt   = {2002/02/01 10:00},
  medline-da     = {20020131},
  medline-dcom   = {20020503},
  medline-edat   = {2002/02/01 10:00},
  medline-fau    = {Trott, Oleg ; Palmer, Arthur G 3rd},
  medline-gr     = {GM59273/GM/NIGMS NIH HHS/United States},
  medline-is     = {1090-7807 (Print) ; 1090-7807 (Linking)},
  medline-jid    = {9707935},
  medline-jt     = {Journal of magnetic resonance (San Diego, Calif. :
                   1997)},
  medline-lr     = {20071114},
  medline-mhda   = {2002/05/04 10:01},
  medline-own    = {NLM},
  medline-pl     = {United States},
  medline-pmid   = {11820837},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article ; Research Support, U.S. Gov't, P.H.S.},
  medline-rn     = {0 (Solutions)},
  medline-sb     = {IM},
  medline-so     = {J Magn Reson. 2002 Jan;154(1):157-60.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=11820837},
  doi            = {10.1006/jmre.2001.2466},
  year           = 2002
}

@Article{TrottPalmer04,
  Author         = {Trott, O. and Palmer, 3rd, A. G.},
  Title          = {Theoretical study of {R}(1rho) rotating-frame and {R}2
                   free-precession relaxation in the presence of n-site
                   chemical exchange.},
  Journal        = jmr,
  Volume         = {170},
  Number         = {1},
  Pages          = {104-112},
  abstract       = {The n-site Bloch-McConnell equations describe the
                   evolution of nuclear spin magnetization in the
                   laboratory or rotating frames of reference for
                   molecules subject to chemical or conformational
                   interconversions between n species with distinct NMR
                   chemical shifts. Perturbation theory is used to
                   approximate the largest eigenvalue of the
                   Bloch-McConnell equations and obtain analytical
                   expressions for the rotating-frame relaxation rate
                   constant and for the laboratory frame resonance
                   frequency and transverse relaxation rate constant. The
                   perturbation treatment is valid whenever the population
                   of one site is dominant. The new results are generally
                   applicable to investigations of kinetic processes by
                   NMR spectroscopy.},
  authoraddress  = {Department of Biochemistry and Molecular Biophysics,
                   Columbia University, 630 West 168th Street, New York,
                   NY 10032, USA.},
  keywords       = {*Models, Chemical ; Nuclear Magnetic Resonance,
                   Biomolecular/*methods ; Proteins/chemistry},
  language       = {eng},
  medline-aid    = {10.1016/j.jmr.2004.06.005 [doi] ; S1090780704001752
                   [pii]},
  medline-crdt   = {2004/08/25 05:00},
  medline-da     = {20040824},
  medline-dcom   = {20041021},
  medline-edat   = {2004/08/25 05:00},
  medline-fau    = {Trott, Oleg ; Palmer, Arthur G 3rd},
  medline-gr     = {GM59273/GM/NIGMS NIH HHS/United States ; T32
                   DK07328/DK/NIDDK NIH HHS/United States},
  medline-is     = {1090-7807 (Print) ; 1090-7807 (Linking)},
  medline-jid    = {9707935},
  medline-jt     = {Journal of magnetic resonance (San Diego, Calif. :
                   1997)},
  medline-lr     = {20071114},
  medline-mhda   = {2004/10/22 09:00},
  medline-own    = {NLM},
  medline-phst   = {2004/03/13 [received] ; 2004/06/10 [revised]},
  medline-pl     = {United States},
  medline-pmid   = {15324763},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article ; Research Support, U.S. Gov't, P.H.S.},
  medline-rn     = {0 (Proteins)},
  medline-sb     = {IM},
  medline-so     = {J Magn Reson. 2004 Sep;170(1):104-12.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=15324763},
  doi            = {10.1016/j.jmr.2004.06.005},
  year           = 2004
}

@Article{Tsan00,
  Author         = {Tsan, P. and Hus, J. C. and Caffrey, M. and Marion, D.
                   and Blackledge, M.},
  Title          = {Rotational diffusion anisotropy and local backbone
                   dynamics of carbon monoxide-bound {\em{R}hodobacter
                   capsulatus} cytochrome c2},
  Journal        = jacs,
  Volume         = {122},
  Number         = {23},
  Pages          = {5603-5612},
  abstract       = {The rotational diffusion and backbone dynamics of the
                   carbon monoxide-bound Rhodobacter capsulatus cytochrome
                   c' have been investigated using heteronuclear NMR
                   spectroscopy. This protein consists of a four-helix
                   bundle motif and a histidine-heme binding domain and
                   has been shown to form a symmetric dimer in the crystal
                   state. N-15 relaxation measurements reveal that an
                   asymmetric tensor is necessary to describe overall
                   rotational diffusion of the protein, showing a
                   significant improvement compared to analysis using
                   either isotropic and axially symmetric tensors. This
                   analysis indicates that the molecule undergoes
                   significant anisotropic reorientation with a diffusion
                   tensor having principal components \{1.37 +/- 0.05,
                   1.68 +/- 0.05, 2.13 +/- 0.07\} x 10(7) s-(1).
                   Hydrodynamic calculations performed on the crystal
                   structure predict values of \{1.400, 1.45, 2.12\} x
                   10(7) s(-1) when a solvent shell of 3.0 Angstrom is
                   included in the calculation. Comparison of the
                   principal axes with the symmetry axes of the dimeric
                   structure derived from X-ray crystallography provides
                   unambiguous evidence that the molecule is monomeric in
                   the solution state. Lipari-Szabo-type mobility
                   parameters extracted when using the anisotropic
                   description of overall tumbling are found to differ
                   considerably from those found assuming isotropic global
                   reorientation, where the internal dynamics of NH
                   vectors present in helical regions of the molecule
                   exhibit clear periodicity due to their orientation
                   relative to the diffusion tensor. In addition, the
                   relaxation properties of helix I are less well
                   reproduced than those of the other three helices,
                   implying a different orientation of this helix compared
                   to that found in the crystal state, possibly due to the
                   volume of the different ligands present in the two
                   forms of the protein. Using restrained molecular
                   dynamics and energy minimization with respect to the
                   relaxation rate ratios, we have quantified the
                   difference in the orientation of this helix and find
                   that a significant reorientation is necessary to
                   fulfill the measured relaxation rates.},
  address        = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
  authoraddress  = {CEA, Jean Pierre Ebel CNRS, Inst Biol Struct, F-38027
                   Grenoble, France.},
  citedref       = {ABRAGAM A, 1961, PRINCIPLES NUCL MAGN ; ARCHER M,
                   1997, J BIOL INORG CHEM, V2, P611 ; BARBATO G, 1992,
                   BIOCHEMISTRY-US, V31, P5269 ; BARTSCH RG, 1978,
                   PHOTOSYNTHETIC BACTE, P249 ; BERENDSEN HJC, 1984, J
                   CHEM PHYS, V81, P3684 ; BLACKLEDGE M, 1998, J AM CHEM
                   SOC, V120, P4538 ; BRUSCHWEILER R, 1995, SCIENCE, V268,
                   P886 ; CAFFREY M, 1995, BIOCHEMISTRY-US, V34, P5904 ;
                   CLORE GM, 1990, J AM CHEM SOC, V112, P4989 ; CORDIER F,
                   1998, J MOL BIOL, V281, P341 ; CUSANOVICH MA, 1971,
                   BIOCHIM BIOPHYS ACTA, V236, P238 ; CUSANOVICH MA, 1988,
                   ADV INORG BIOCHEM, V7, P37 ; DELATORRE JG, 1981, Q REV
                   BIOPHYS, V14, P81 ; DEVORE J, 1982, PROBABILITY STAT
                   ENG ; DOBBS AJ, 1996, ACTA CRYSTALLOGR D 2, V52, P356 ;
                   DOSSET P, 2000, J BIOMOL NMR, V16, P23 ; DOYLE ML,
                   1986, BIOCHEMISTRY-US, V25, P2509 ; FARROW NA, 1994,
                   BIOCHEMISTRY-US, V33, P5984 ; FINZEL BC, 1985, J MOL
                   BIOL, V186, P627 ; HUS JC, 1999, J AM CHEM SOC, V121,
                   P2311 ; KASSNER RJ, 1985, BIOCHIM BIOPHYS ACTA, V831,
                   P155 ; KAY LE, 1989, BIOCHEMISTRY-US, V28, P8972 ; LEE
                   B, 1971, J MOL BIOL, V55, P379 ; LEE LK, 1997, J BIOMOL
                   NMR, V9, P287 ; LIPARI G, 1982, J AM CHEM SOC, V104,
                   P4546 ; LIPARI G, 1982, J AM CHEM SOC, V104, P4559 ;
                   MEYER TE, 1982, ADV PROTEIN CHEM, V35, P105 ; MOORE GR,
                   1990, CYTOCHROMES C MINUS ; OREKHOV VY, 1995, APPL MAGN
                   RESON, V9, P581 ; PATEL MJ, 1989, BIOCHEMISTRY-US, V28,
                   P2140 ; PEARLMAN DA, 1991, AMBER 4 0 ; PENG JW, 1992,
                   BIOCHEMISTRY-US, V31, P8571 ; PENG JW, 1995,
                   BIOCHEMISTRY-US, V34, P16733 ; REN Z, 1993, J MOL BIOL,
                   V234, P433 ; SCHURR JM, 1994, J MAGN RESON SER B, V105,
                   P211 ; SHIBATA N, 1998, J MOL BIOL, V284, P751 ; SINGH
                   UC, 1984, J COMPUT CHEM, V5, P129 ; TAHIROV TH, 1996, J
                   MOL BIOL, V259, P467 ; TAHIROV TH, 1996, NAT STRUCT
                   BIOL, V3, P459 ; TANIGUCHI S, 1963, BIOCHIM BIOPHYS
                   ACTA, V74, P438 ; TJANDRA N, 1995, J AM CHEM SOC, V117,
                   P12562 ; TJANDRA N, 1996, J BIOMOL NMR, V8, P273 ; TSAN
                   P, 1998, THESIS U J FOURIER G ; WEBER PC, 1981, J MOL
                   BIOL, V153, P399 ; WOESSNER DE, 1962, J CHEM PHYS, V37,
                   P647 ; YAZUI M, 1992, J BIOCH, V111, P317 ; ZHENG Z,
                   1995, BIOCHEMISTRY-US, V34, P5212},
  isifile-dt     = {Article},
  isifile-ga     = {327KK},
  isifile-j9     = {J Am Chem Soc},
  isifile-ji     = {J. Am. Chem. Soc.},
  isifile-nr     = {47},
  isifile-pi     = {WASHINGTON},
  isifile-rp     = {Blackledge, M, CEA, Jean Pierre Ebel CNRS, Inst Biol
                   Struct, 41 Rue ; Jules Horowitz, F-38027 Grenoble,
                   France.},
  isifile-sc     = {Chemistry, Multidisciplinary},
  isifile-tc     = {15},
  issn           = {0002-7863},
  keywords       = {[ISI:] n-15 nmr relaxation; model-free approach;
                   magnetic-resonance relaxation; ferricytochrome c';
                   chromatium-vinosum; crystal-structure; eglin-c;
                   macromolecules; resolution; proteins ;;},
  language       = {English},
  month          = {Jun 14},
  publisher      = {Amer Chemical Soc},
  size           = {10 p.},
  sourceid       = {ISI:000087792900023},
  year           = 2000
}

@Article{Tugarinov01,
  Author         = {Tugarinov, V. and Liang, Z. and Shapiro, Y. E. and
                   Freed, J. H. and Meirovitch, E.},
  Title          = {A structural mode-coupling approach to 15{N} {NMR}
                   relaxation in proteins.},
  Journal        = jacs,
  Volume         = {123},
  Number         = {13},
  Pages          = {3055-3063},
  abstract       = {The two-body Slowly Relaxing Local Structure (SRLS)
                   model was applied to (15)N NMR spin relaxation in
                   proteins and compared with the commonly used original
                   and extended model-free (MF) approaches. In MF, the
                   dynamic modes are assumed to be decoupled, local
                   ordering at the N-H sites is represented by generalized
                   order parameters, and internal motions are described by
                   effective correlation times. SRLS accounts for
                   dynamical coupling between the global diffusion of the
                   protein and the internal motion of the N-H bond vector.
                   The local ordering associated with the coupling
                   potential and the internal N-H diffusion are tensors
                   with orientations that may be tilted relative to the
                   global diffusion and magnetic frames. SRLS generates
                   spectral density functions that differ from the MF
                   formulas. The MF spectral densities can be regarded as
                   limiting cases of the SRLS spectral density. SRLS-based
                   model-fitting and model-selection schemes similar to
                   the currently used MF-based ones were devised, and a
                   correspondence between analogous SRLS and model-free
                   parameters was established. It was found that
                   experimental NMR data are sensitive to the presence of
                   mixed modes. Our results showed that MF can
                   significantly overestimate order parameters and
                   underestimate local motion correlation times in
                   proteins. The extent of these digressions in the
                   derived microdynamic parameters is estimated in the
                   various parameter ranges, and correlated with the time
                   scale separation between local and global motions. The
                   SRLS-based analysis was tested extensively on (15)N
                   relaxation data from several isotropically tumbling
                   proteins. The results of SRLS-based fitting are
                   illustrated with RNase H from E. coli, a protein
                   extensively studied previously with MF.},
  authoraddress  = {Faculty of Life Sciences, Bar-Ilan University,
                   Ramat-Gan 52900, Israel.},
  keywords       = {Comparative Study ; Diffusion ; Nitrogen Isotopes ;
                   Nuclear Magnetic Resonance, Biomolecular/*methods ;
                   Proteins/*chemistry ; Research Support, Non-U.S. Gov't
                   ; Research Support, U.S. Gov't, P.H.S. ; Thermodynamics},
  language       = {eng},
  medline-aid    = {ja003803v [pii]},
  medline-da     = {20010717},
  medline-dcom   = {20010906},
  medline-edat   = {2001/07/18 10:00},
  medline-fau    = {Tugarinov, V ; Liang, Z ; Shapiro, Y E ; Freed, J H ;
                   Meirovitch, E},
  medline-gr     = {RR07126/RR/NCRR},
  medline-is     = {0002-7863},
  medline-jid    = {7503056},
  medline-lr     = {20041117},
  medline-mhda   = {2001/09/08 10:01},
  medline-own    = {NLM},
  medline-pl     = {United States},
  medline-pmid   = {11457016},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Nitrogen Isotopes) ; 0 (Proteins)},
  medline-sb     = {IM},
  medline-so     = {J Am Chem Soc 2001 Apr 4;123(13):3055-63.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=11457016},
  year           = 2001
}

@Article{VanGeet70,
  Author         = {VanGeet, A. L.},
  Title          = {Calibration of methanol nuclear magnetic resonance
                   thermometer at low temperature},
  Journal        = ac,
  Volume         = {42},
  Number         = {6},
  Pages          = {679-680},
  sourceid       = {ISI:A1970G041900033},
  year           = 1970
}

@Article{Viles01,
  author = {Viles, John and Duggan, Brendan and Zaborowski, Eduardo and Schwarzinger, Stephan and Huntley, James and Kroon, Gerard and Dyson, H.Jane and Wright, Peter},
  title = {Potential bias in {NMR} relaxation data introduced by peak intensity analysis and curve fitting methods},
  journal = jbnmr,
  publisher = {Springer Netherlands},
  issn = {0925-2738},
  keyword = {Physics and Astronomy},
  pages = {1-9},
  volume = {21},
  issue = {1},
  url = {http://dx.doi.org/10.1023/A:1011966718826},
  doi = {10.1023/A:1011966718826},
  abstract = {We present an evaluation of the accuracy and precision of relaxation rates calculated using a variety of methods, applied to data sets obtained for several very different protein systems. We show that common methods of data evaluation, such as the determination of peak heights and peak volumes, may be subject to bias, giving incorrect values for quantities such as R1 and R2. For example, one common method of peak-height determination, using a search routine to obtain the peak-height maximum in successive spectra, may be a source of significant systematic error in the relaxation rate. The alternative use of peak volumes or of a fixed coordinate position for the peak height in successive spectra gives more accurate results, particularly in cases where the signal/noise is low, but these methods have inherent problems of their own. For example, volumes are difficult to quantitate for overlapped peaks. We show that with any method of sampling the peak intensity, the choice of a 2- or 3-parameter equation to fit the exponential relaxation decay curves can dramatically affect both the accuracy and precision of the calculated relaxation rates. In general, a 2-parameter fit of relaxation decay curves is preferable. However, for very low intensity peaks a 3 parameter fit may be more appropriate.},
  year = {2001}
}

@Article{Wallach67,
  Author         = {Wallach, Daniel},
  Title          = {Effect of internal rotation on angular correlation
                   functions},
  Journal        = jcp,
  Volume         = {47},
  Number         = {12},
  Pages          = {5258-5268},
  abstract       = {Fluorescence polarization, nuclear magnetic resonance,
                   and electron spin resonance experiments on
                   appropriately labeled proteins give information about
                   various angular correlation functions or correlation
                   times for the reorientation of the label. Expressions
                   are derived relating these correlation functions and
                   times to the rotation rate of the rigid protein and the
                   rates of the internal rotations between the label and
                   the protein. The effective correlation time for the
                   label is simply a series of factors times the
                   correlation time for the rigid protein. Each internal
                   rotation which is much faster than the protein rotation
                   contributes a single factor \frac1/2{}(3 cos2theta-1)2,
                   where theta is the angle from the internal rotation
                   axis of interest to the next internal rotation axis,
                   or, for the last internal rotation, to the label axis
                   of interest. The effect of internal rotations which are
                   much slower than the protein rotation rate is the same
                   as the effect of averaging over molecules with a
                   permanent geometry corresponding to the possible
                   orientations about the internal rotation axis.},
  collaboration  = {},
  publisher      = {AIP},
  url            = {http://link.aip.org/link/?JCP/47/5258/1},
  year           = 1967
}

@Article{WittebortSzabo78,
  Author         = {Wittebort, R. J. and Szabo, Attila},
  Title          = {Theory of {NMR} relaxation in macromolecules:
                   {R}estricted diffusion and jump models for multiple
                   internal rotations in amino acid side chains},
  Journal        = jcp,
  Volume         = {69},
  Number         = {4},
  Pages          = {1722-1736},
  abstract       = {The theory required to extract detailed motional
                   information from NMR relaxation times of nuclei in an
                   amino acid side chain containing multiple internal
                   rotation axes attached to a large macromolecule of at
                   least cylindrical symmetry is developed. Emphasis is
                   placed on the analysis of 13C-NMR of protonated carbons
                   where dipolar relaxation is predominant. Extension to
                   other relaxation processes is straightforward. The
                   spectral density from which the relaxation times can be
                   calculated is obtained for various models for the
                   motion of the side chain. The existing theory which
                   assumes that internal rotations are both independent
                   and free is generalized to incorporate excluded volume
                   effects in a heuristic way by restricting the amplitude
                   of the internal rotations. It is found that small
                   amplitude motions are ineffective in causing
                   relaxation. Thus jump models involving a relatively
                   small number of configurations are appropriate to
                   describe the motion of the side chain. The advantage of
                   jump models is twofold: (1) excluded volume effects can
                   be handled simply by including only sterically allowed
                   configurations, and (2) the unrealistic assumption of
                   diffusional models that rotations about different bonds
                   are independent can be removed by considering concerted
                   motions in which the positions of only a small number
                   of atoms are altered. An explicit expression for the
                   spectral density, which is computationally practical
                   when the number of configurations is less than 200, is
                   obtained for a class of jump models in which the
                   dynamics is described by a master equation. A detailed
                   application of the general formalism is made to the
                   case of a lysine side chain whose carbon-carbon
                   backbone is constrained to lie on a tetrahedral
                   lattice. Finally, numerical calculations are presented
                   to illustrate some of the qualitative features of the
                   different models, and the strategy that can be used to
                   obtain motional information from experiment within the
                   framework of these models is discussed.},
  collaboration  = {},
  publisher      = {AIP},
  url            = {http://link.aip.org/link/?JCP/69/1722/1},
  year           = 1978
}

@Article{Woessner62,
  Author         = {Woessner, D. E.},
  Title          = {Nuclear spin relaxation in ellipsoids undergoing
                   rotational brownian motion},
  Journal        = jcp,
  Volume         = {37},
  Number         = {3},
  Pages          = {647-654},
  address        = {Circulation Fulfillment Div, 500 Sunnyside Blvd,
                   Woodbury, NY 11797-2999},
  citedref       = {BLICHARSKI JS, 1960, B AMPERE, P452 ; BLOEMBERGEN N,
                   1948, PHYS REV, V73, P679 ; BLOOM M, 1961, CAN J PHYS,
                   V39, P1093 ; DALE LF, 1960, PHYS REV, V119, P53 ;
                   GOLDSTEIN H, 1950, CLASSICAL MECH, P107 ; HILL NE,
                   1954, P PHYS SOC B, V67, P149 ; HUBBARD PS, 1961, REV
                   MOD PHYS, V33, P249 ; KUBO R, 1954, J PHYS SOC JPN, V9,
                   P888 ; MEAKINS RJ, 1958, T FARADAY SOC, V54, P1160 ;
                   MITCHELL RW, 1960, J CHEM PHYS, V33, P86 ; MITCHELL RW,
                   1961, J CHEM PHYS, V34, P651 ; PERRIN F, 1934, J
                   PHYS-PARIS, V5, P497 ; PERRIN F, 1936, J PHYS-PARIS,
                   V7, P1 ; POWLES JG, 1961, P PHYS SOC LOND, V78, P377 ;
                   SMYTH CP, 1955, DIELECTRIC BEHAVIOR, P99 ; SOLOMON I,
                   1955, PHYS REV, V99, P559 ; WOESSNER DE, 1962, J CHEM
                   PHYS, V36, P1},
  isifile-dt     = {Article},
  isifile-ga     = {4141B},
  isifile-j9     = {J Chem Phys},
  isifile-ji     = {J. Chem. Phys.},
  isifile-nr     = {17},
  isifile-pi     = {Woodbury},
  isifile-sc     = {Physics, Atomic, Molecular \& Chemical},
  isifile-tc     = {904},
  issn           = {0021-9606},
  language       = {English},
  publisher      = {Amer Inst Physics},
  size           = {0 p.},
  sourceid       = {ISI:A19624141B00048},
  doi            = {10.1063/1.1701390},
  year           = 1962
}

@Article{Wright05,
  Author         = {Wright, N.T. and Margolis, J.W. and Margolis, F.L. and
                   Weber, D.J.},
  Title          = {Refinement of the solution structure of rat olfactory
                   marker protein ({OMP}).},
  Journal        = jbnmr,
  Volume         = {33},
  Number         = {1},
  Pages          = {63-68},
  authoraddress  = {Department of Biochemistry and Molecular Biology,
                   University of Maryland School of Medicine, Baltimore,
                   Maryland 21201, USA.},
  language       = {eng},
  doi            = {10.1007/s10858-005-1281-7},
  medline-aid    = {10.1007/s10858-005-1281-7 [doi]},
  medline-da     = {20051013},
  medline-edat   = {2005/10/14 09:00},
  medline-fau    = {Wright, Nathan T ; Margolis, Joyce W ; Margolis, Frank
                   L ; Weber, David J},
  medline-gr     = {DC03112/DC/NIDCD ; GM58888/GM/NIGMS ;
                   T32-AR07592/AR/NIAMS},
  medline-is     = {0925-2738 (Print)},
  medline-jid    = {9110829},
  medline-jt     = {Journal of biomolecular NMR.},
  medline-mhda   = {2005/10/14 09:00},
  medline-own    = {NLM},
  medline-phst   = {2005/05/26 [received] ; 2005/07/15 [accepted]},
  medline-pl     = {Netherlands},
  medline-pmid   = {16222559},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-sb     = {IM},
  medline-so     = {J Biomol NMR. 2005 Sep;33(1):63-8.},
  medline-stat   = {In-Process},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=16222559},
  year           = 2005
}

@Article{Zheng95,
  Author         = {Zheng, Z. and Czaplicki, J. and Jardetzky, O.},
  Title          = {Backbone dynamics of trp repressor studied by 15{N}
                   {NMR} relaxation.},
  Journal        = biochem,
  Volume         = {34},
  Number         = {15},
  Pages          = {5212-5223},
  abstract       = {Backbone dynamics of trp repressor, a 25 kDa DNA
                   binding protein, have been studied using 15N relaxation
                   data measured by proton-detected two-dimensional 1H-15N
                   NMR spectroscopy. 15N spin-lattice relaxation time
                   (T1), spin-spin relaxation time (T2), and heteronuclear
                   NOEs were determined for all visible backbone amide 15N
                   nuclei. Monte Carlo simulations of the amplitudes of
                   backbone motions led to the conclusion that a wobbling
                   in a cone model with consideration of the anisotropic
                   reorientation of the molecule was appropriate to
                   describe the underlying motions, allowing us to derive
                   the semiangle of the cone (alpha) and the effective
                   correlation time for internal motions (tau e) for each
                   N-H bond vector. The final optimized rotational
                   diffusion coefficients parallel (D parallel) and
                   perpendicular (D perpendicular) to the unique axis of
                   the molecule were found to be 1.48 +/- 0.06 x 10(7) and
                   1.15 +/- 0.05 x 10(7) s-1, respectively. The average
                   semiangle of the cone (alpha) describing the amplitude
                   of NH vector motions on the picosecond time scale was
                   found to be 20.9 +/- 5.7 degrees. Large amplitude
                   motions on the picosecond time scale are found at both
                   the N and C termini but are restricted in both the
                   hydrophobic core and DNA-binding regions.},
  authoraddress  = {Stanford Magnetic Resonance Laboratory, Stanford
                   University, California 94305-5055, USA.},
  keywords       = {Anisotropy ; *Bacterial Proteins ; Hydrogen ; Magnetic
                   Resonance Spectroscopy ; Models, Chemical ; Models,
                   Molecular ; Motion ; Nitrogen Isotopes ; Protein
                   Conformation ; Repressor Proteins/*chemistry ; Research
                   Support, U.S. Gov't, P.H.S.},
  language       = {eng},
  medline-da     = {19950517},
  medline-dcom   = {19950517},
  medline-edat   = {1995/04/18},
  medline-fau    = {Zheng, Z ; Czaplicki, J ; Jardetzky, O},
  medline-gr     = {GM33385/GM/NIGMS ; RR07558/RR/NCRR},
  medline-is     = {0006-2960},
  medline-jid    = {0370623},
  medline-lr     = {20041117},
  medline-mhda   = {1995/04/18 00:01},
  medline-own    = {NLM},
  medline-pl     = {UNITED STATES},
  medline-pmid   = {7711041},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (Bacterial Proteins) ; 0 (Nitrogen Isotopes) ; 0
                   (Repressor Proteins) ; 0 (tryptophan repressor protein)
                   ; 1333-74-0 (Hydrogen)},
  medline-sb     = {IM},
  medline-so     = {Biochemistry 1995 Apr 18;34(15):5212-23.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=7711041},
  year           = 1995
}

@Article{Zhuravleva04,
  Author         = {Zhuravleva, A. V. and Korzhnev, D. M. and Kupce, E.
                   and Arseniev, A. S. and Billeter, M. and Orekhov, V. Y.},
  Title          = {Gated electron transfers and electron pathways in
                   azurin: a {NMR} dynamic study at multiple fields and
                   temperatures.},
  Journal        = jmb,
  Volume         = {342},
  Number         = {5},
  Pages          = {1599-1611},
  abstract       = {Dynamic properties of electron transfer pathways in a
                   small blue copper cupredoxin are explored using an
                   extensive 15N NMR relaxation study of reduced
                   Pseudomonas aeruginosa azurin at four magnetic fields
                   (500-900 MHz) and at two temperatures chosen well below
                   the melting point of the protein. Following a careful
                   model-free analysis, several protein regions with
                   different dynamic regimes are identified. Nanosecond
                   time-scale mobility characterizes various residues of
                   the hydrophobic surface patch believed to mark the
                   natural entry point for electrons, notably the
                   surface-exposed copper-ligand His117. These findings
                   are consistent with a gated electron transfer process
                   according to the "dynamic docking" model. Residues
                   47-49 along intramolecular pathways of electrons show
                   rigidity that is remarkably conserved when increasing
                   the temperature. Three different conformational
                   exchange processes were observed in the millisecond
                   range, one near the only disulfide bridge in the
                   molecule and two near the copper ion. The latter two
                   processes are consistent with previous data such as
                   crystal structures at various pH values and NMR
                   relaxation dispersion experiments; they may indicate an
                   additional gated electron transfer mechanism at slower
                   time-scales.},
  authoraddress  = {Swedish NMR Centre, Goteborg University, Box 465, 405
                   30 Goteborg, Sweden.},
  keywords       = {Azurin/*analogs \& derivatives/*chemistry/*metabolism
                   ; Copper/*metabolism ; Electron Transport ; *Electrons
                   ; Kinetics ; Nuclear Magnetic Resonance,
                   Biomolecular/*methods ; Oxidation-Reduction ; Protein
                   Conformation ; Pseudomonas
                   aeruginosa/chemistry/*metabolism ; Research Support,
                   Non-U.S. Gov't ; Temperature ; Thermodynamics},
  language       = {eng},
  doi            = {10.1016/j.jmb.2004.08.001},
  medline-aid    = {10.1016/j.jmb.2004.08.001 [doi] ;
                   S0022-2836(04)00955-6 [pii]},
  medline-da     = {20040914},
  medline-dcom   = {20041101},
  medline-edat   = {2004/09/15 05:00},
  medline-fau    = {Zhuravleva, Anastasia V ; Korzhnev, Dmitry M ; Kupce,
                   Eriks ; Arseniev, Alexander S ; Billeter, Martin ;
                   Orekhov, Vladislav Yu},
  medline-is     = {0022-2836},
  medline-jid    = {2985088R},
  medline-lr     = {20041117},
  medline-mhda   = {2004/11/02 09:00},
  medline-own    = {NLM},
  medline-phst   = {2004/05/09 [received] ; 2004/07/02 [revised] ;
                   2004/08/01 [accepted]},
  medline-pl     = {England},
  medline-pmid   = {15364584},
  medline-pst    = {ppublish},
  medline-pt     = {Journal Article},
  medline-pubm   = {Print},
  medline-rn     = {0 (cupredoxin) ; 12284-43-4 (Azurin) ; 7440-50-8
                   (Copper)},
  medline-sb     = {IM},
  medline-so     = {J Mol Biol 2004 Oct 1;342(5):1599-611.},
  medline-stat   = {MEDLINE},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=15364584},
  year           = 2004
}

@Article{Zucchini00,
  Author         = {Zucchini, W.},
  Title          = {An Introduction to Model Selection.},
  Journal        = jmp,
  Volume         = {44},
  Number         = {1},
  Pages          = {41-61},
  abstract       = {This paper is an introduction to model selection
                   intended for nonspecialists who have knowledge of the
                   statistical concepts covered in a typical first
                   (occasionally second) statistics course. The intention
                   is to explain the ideas that generate frequentist
                   methodology for model selection, for example the Akaike
                   information criterion, bootstrap criteria, and
                   cross-validation criteria. Bayesian methods, including
                   the Bayesian information criterion, are also mentioned
                   in the context of the framework outlined in the paper.
                   The ideas are illustrated using an example in which
                   observations are available for the entire population of
                   interest. This enables us to examine and to measure
                   effects that are usually invisible, because in
                   practical applications only a sample from the
                   population is observed. The problem of selection bias,
                   a hazard of which one needs to be aware in the context
                   of model selection, is also discussed. Copyright 2000
                   Academic Press.},
  authoraddress  = {University of Gottingen},
  language       = {ENG},
  doi            = {10.1006/jmps.1999.1276},
  medline-aid    = {10.1006/jmps.1999.1276 [doi] ; jmps.1999.1276 [pii]},
  medline-da     = {20000327},
  medline-edat   = {2000/03/29},
  medline-is     = {0022-2496},
  medline-mhda   = {2000/03/29},
  medline-own    = {NLM},
  medline-pmid   = {10733857},
  medline-pst    = {ppublish},
  medline-pt     = {JOURNAL ARTICLE},
  medline-pubm   = {Print},
  medline-so     = {J Math Psychol 2000 Mar;44(1):41-61.},
  medline-stat   = {Publisher},
  url            = {http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=10733857},
  year           = 2000
}

