When the Multalign Viewer option Structure... Secondary Structure... show predicted or the MSF Viewer option Style... Secondary Structure is chosen, secondary structure is predicted for individual sequences using the method described in:
J. Garnier, D.J. Osguthorpe, and B. Robson, "Analysis of the Accuracy and Implications of Simple Methods for Predicting the Secondary Structure of Globular Proteins" J. Mol. Biol. 120:97 (1978).This method, generally referred to as GOR (based on authors' last initials), is used with the newer single-residue parameters given in:
J.-F. Gibrat, J. Garnier, and B. Robson, "Further Developments of Protein Secondary Structure Prediction Using Information Theory" J. Mol. Biol. 198:425 (1987).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%.