Patent ID: 6490532
Filing Date: 2002-12-03
Classification: G16B

Abstract:
A computer-imnplemented method for identifying at least one conformation of a protein of known or unknown structure which comprises the steps of:(a) providing an amino acid sequence of the protein; (b) constructing, a backbone structure of &agr;-carbons of the amino acid sequence of the protein by adding and removing carbon atoms through chain elongation and backtracking, which comprises randomly sampling trajectory distributions represerning a statistical sampling from each amino acid of the conformational space it is observed to visit in known proteins, and backtracking using a hierarchical data structure to remove a& atom if it is closer to its neighbor than allowed by van der Waals radii; (c) positioning &bgr; carbons, C, N, and O atoms about the constructed backbone structure of step (b) wherein the atoms are positioned to provide favourable bond lengths and bond angles; (d) positioning sidechain rotamers including adding hydrogen atoms; and (e) displaying the results of steps (a)-(d); thereby outputting at least one conformation of the protein.