Secondary Structure Predictions with GOR

The Multalign Viewer menu setting Structure... Secondary Structure... show predicted shows regions named predicted helices (gold outline) and predicted strands (green outline) in sequences not associated with structures.

These predictions are generated for individual sequences using the method described in:

Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. Garnier J, Osguthorpe DJ, Robson B. J Mol Biol. 1978 Mar 25;120(1):97-120.
This method, generally referred to as GOR (based on authors' last initials), is used with the newer single-residue parameters given in:
Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. Gibrat JF, Garnier J, Robson B. J Mol Biol. 1987 Dec 5;198(3):425-43.
The residue-pair parameters introduced in the latter paper are not used. The single-residue approximation alone yielded 56% accuracy, whereas addition of the residue-pair parameters increased the accuracy to 63%.

UCSF Computer Graphics Laboratory / December 2009