When the Multalign Viewer option Structure... Secondary Structure... show predicted 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%.