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.
Read more about this topic: GOR Method
Famous quotes containing the word method:
“The most passionate, consistent, extreme and implacable enemy of the Enlightenment and ... all forms of rationalism ... was Johann Georg Hamann. His influence, direct and indirect, upon the romantic revolt against universalism and scientific method ... was considerable and perhaps crucial.”
—Isaiah Berlin (b. 1909)
“Women are denied masturbation even more severely than men and that’s another method of control—they’re not taught to please themselves.... Most women—it takes them a while to warm up to the “situation” but once they get into it, I’m sure they’re going to get just as hooked as—well, everyone I know is!”
—Lydia Lunch (b. 1959)
“The country needs and, unless I mistake its temper, the country demands bold, persistent experimentation. It is common sense to take a method and try it. If it fails, admit it frankly and try another. But above all, try something. The millions who are in want will not stand idly by silently forever while the things to satisfy their needs are within easy reach.”
—Franklin D. Roosevelt (1882–1945)