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GOR method
The GOR method (Garnier-Osguthorpe-Robson) is an information theory-based method for the prediction of secondary structures in proteins.〔Garnier J, Gibrat JF, Robson B. (1996). GOR method for predicting protein secondary structure from amino acid sequence. (''Methods Enzymol'' 266:540-53 ).〕 It was developed in the late 1970s shortly after the simpler Chou-Fasman method. Like Chou-Fasman, the GOR method is based on probability parameters derived from empirical studies of known protein tertiary structures solved by X-ray crystallography. However, unlike Chou-Fasman, the GOR method takes into account not only the propensities of individual amino acids to form particular secondary structures, but also the conditional probability of the amino acid to form a secondary structure given that its immediate neighbors have already formed that structure. The method is therefore essentially Bayesian in its analysis.〔Garnier J, Osguthorpe DJ, Robson B. (1978). Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. (''J Mol Biol'' 120:97-120 ).〕
==Method==
The GOR method analyzes sequences to predict alpha helix, beta sheet, turn, or random coil secondary structure at each position based on 17-amino-acid sequence windows. The original description of the method included four scoring matrices of size 17×20, where the columns correspond to the log-odds score, which reflects the probability of finding a given amino acid at each position in the 17-residue sequence. The four matrices reflect the probabilities of the central, ninth amino acid being in a helical, sheet, turn, or coil conformation. In subsequent revisions to the method, the turn matrix was eliminated due to the high variability of sequences in turn regions (particularly over such a large window). The method was considered as best requiring at least four contiguous residues to score as alpha helices to classify the region as helical, and at least two contiguous residues for a beta sheet.〔Mount DM (2004). ''Bioinformatics: Sequence and Genome Analysis'', 2, Cold Spring Harbor Laboratory Press. ISBN 0-87969-712-1.〕
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