Structure : Predict Secondary Structure
Predict Protein Secondary Structure
This popup window is designed to allow the prediction of secondary structure
for a protein chain given chemical shifts, using the (external) program D2D.
The Options to select are the Chain and the Shift List, for which the
prediction is then made.
The Secondary Structure Predictions table lists the residues in the chain.
For each residue the residue number, residue type and current secondary
structure set for that residue is given. The remaining columns are for
the predictions made by D2D, and of course are only filled in once D2D
is run. The predicted secondary structure is listed first, followed by
the probability of that residue being Helix, Beta, Coil or PPII (the
predicted secondary structure will be specified by the maximum of these).
To run the prediction click on the “Run D2D Prediction!” button. This
does not store this information in the project. To do that you have to
click on the “Commit Predicted Secondary Structure” button.
Caveats & Tips
The predicted secondary structure cell is coloured red if the prediction
is unreliable. Unreliable predictions are not stored with the “Commit”
button but all reliable ones are. If you need to edit the secondary
structure for a residue then use the Secondary Structure Chart:
References
The D2D programme:
http://www-vendruscolo.ch.cam.ac.uk/d2D/index.php
*C. Camilloni, A. De Simone, W. Vranken and M. Vendruscolo.
Determination of Secondary Structure Populations in Disordered States of Proteins using NMR Chemical Shifts.
Biochemistry 2012, 51: 2224-2231
Main Panel
Options
Chain: Choose the molecular system chain to make predictions for
Shift List: Select the shift list to take input chemical shifts from
Secondary Structure Predictions
Table 1 |
Res Num |
Residue number in chain |
Res Type |
Residue type code |
Current SS |
Current stored secondary structure code |
Predicted SS |
Predicted secondary structure code |
Helix |
Probability residue is Helix |
Beta |
Probability residue is Beta |
Coil |
Probability residue is Coil |
PPII |
Probability residue is PPII |
Run D2D Prediction!: Run the D2D method to predict secondary structure
Commit Predicted Secondary Structure: Store the secondary structure predictions in the CCPN project