Patent ID: 6859736
Filing Date: 2005-02-22
Classification: G16B

Abstract:
1. A program storage device accessible by a computer embodying a program of instructions executable by said computer to perform method steps for protein structure alignment, comprising: (a) receiving atomic coordinates of a first protein with N (b) receiving atomic coordinates of a second protein with N (c) making an initial alignment of said atoms of said first protein to said atoms of said second protein; (d) calculating all atomic distances between said atomic coordinates of said atoms of said first protein and said atomic coordinates of said atoms of said second protein; (e) defining a matrix with a plurality of binary assignment variables wherein each binary assignment variable corresponding to either a match or to a gap; (f) defining one or more mean field equations wherein said plurality of binary assignment variables are replaced by a plurality of continuous mean field variables, whereby said each mean field variable has a value between 0 and 1, and a plurality of forces that are proportional to said atomic distances squared; (g) formulating an energy function, wherein: (h) minimizing by an iterative process of said energy function and updating said continuous mean field variables in said mean field equations for a decreasing set of temperatures T until convergence to a predefined convergence value is reached; and (i) after convergence rounding off said continuous mean field variables to either 0 or 1.