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

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

pulldown 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

button Run D2D Prediction!: Run the D2D method to predict secondary structure

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

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