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.
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