DANGLE

A Bayesian inferential prediction method for protein backbone dihedral angles

DANGLE (Dihedral ANgles from Global Likelihood Estimates) predicts protein backbone Phi and Psi angles and secondary structure assignments solely from amino acid sequence information, experimental chemical shifts and a database of known protein structures and their associated shifts. This approach uses Bayesian inferential logic to analyse the likelihood of conformations throughout Ramachandran space, paying explicit attention to the population distributions expected for different amino acid residue types.

Simple filtering procedures can identify the most “predictable” residues, yielding 92% of all Phi and Psi predictions accurate to within +/-30 degrees. In contrast to previous approaches, more than 80% of Phi or Psi predictions for glycine and pre-proline are reliable. Furthermore, DANGLE provides meaningful upper and lower bounds for the predictions which are shown to represent the precision of the prediction. Over 90% of the experimental dihedral angles in the set of test proteins are within the boundary ranges suggested by DANGLE. At a lower resolution level, the program correctly assigns each residue to one of three secondary structure states (H, E or C) in 85% of cases.

DANGLE also provides an indication of the degeneracy in the relationship between shift measurements and conformation at each site.

For more documentation see the DANGLE web site at SourceForge.

Reference

Ming-Sin Cheung, Mahon L. Maguire, Tim J. Stevens, and R. William Broadhurst. “DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure.” Journal of Magnetic Resonance Volume 202, Issue 2, February 2010, Pages 223-233

Main Panel

Options

pulldown Chain: Choose the molecular system chain to make predictions for

pulldown Shift List: Select the shift list to take input chemical shifts from

pulldown Max No. of Islands: Select the maximum allowed number of disontinuous prediction islands

pulldown Dangle Run: Select a run number to store DANGLE results within

pulldown Ensemble: Select the structure ensemble for superimposition of angle values on the GLE plots

pulldown Restraint Set: Select the CCPN restraint set to store DANGLE dihedral angle restraints in

Global Likelihood Estimates

Scrollbar: :

button Previous: Show GLE plot of angle predictions for previous residue in chain

button Next: Show GLE plot of angle predictions for next residue in chain

Dihedral Angle Predictions

Table 1
Res Num Residue number in chain
Res Type Residue type code
No. of Islands Number of high scoring discontinuous angle predictions
SS Predicted secondary structure code
Phi Predicted phi dihedral angle (CO-N-CA-CO) (Editable)
Psi Predicted psi dihedral angle (N-CA-CO-N) (Editable)
Phi Upper Upper bound of phi angle prediction (Editable)
Phi Lower Lower bound of phi angle prediction (Editable)
Psi Upper Upper bound of psi angle prediction (Editable)
Psi Lower Lower bound of phi angle prediction (Editable)
Chemical Shifts Chemical shifts used in prediction

button Clear Selected: Remove the predictions for the selected residues

button Run Prediction!: Run the DANGLE method to predict dihedral angles and secondary structure

button Delete Current Run: Delete the DANGLE results stored under the current run number

button Commit Restraints: Store the angle predictions and bounds in a new CCPN dihedral angle restraint list

button Commit Secondary Structure: Store the secondary structure predictions in the CCPN project

Table Of Contents

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Structure : Make H Bond Restraints

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Deposition Entry Completion Interface

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