Secondary Structure – Deleage-Roux

The Secondary Structure – Deléage-Roux track predicts secondary structure using the approach of Deléage and Roux, 1987. The method uses an independent prediction of the protein’s structural class to bias the prediction of its secondary structure. Protean 3D begins its calculations by predicting the class of the protein from its amino acid composition. Class designations are identical to those of Nakashima et al., 1986, except for α/ß class proteins. Protean 3D divides α/ß class proteins into two subclasses, α/ß-α and α/ß-ß, according to their distance from the α and ß classes. The letter R is used by Deléage and Roux to designate the “irregular” class of proteins. Next, secondary structure is predicted from the frequency of occurrence of each residue in the four states (helix, sheet, turn and coil) using the secondary structure database of Kabsch and Sander.

To apply this track to the sequence:

In the Tracks panel, expand Secondary Structure and check the box next to Deleage-Roux. The track will now be visible in the Analysis view

To edit track options:

Select the track in the Tracks panel. Open the Track Options section, which appears as follows:

• If you know the structural class for your protein (A, B, A+B, A/B – A, A/B – B, R), choose it by clicking on a button.

• Use the default, Computer Calculated, if you do not know to which class your protein belongs.

Click if you wish to return to the default value.