Patent ID: 6470305
Filing Date: 2002-10-22
Classification: G16C

Abstract:
A method for computing an alignment between a first molecule and a second molecule, the method comprising:(a) providing a set of coordinate points; (b) computing a molecular surface for said first molecule; (c) selecting a first set of points that are approximately equidistant from the computed surface; (d) computing a molecular surface for said second molecule; (e) selecting a second set of points that are approximately equidistant from the computed surface of said second molecule; (f) computing the distance from each selected point to the nearest hydrogen bond acceptor, and the distance from each selected point to the nearest hydrogen bond donor to provide a weighting for each point, said weighting further comprising the computed distance from the point to the computed molecular surface and direction of the hydrogen bond; (g) identifying a first point in said first set having a weighting identical, within a predetermined tolerance, to the weighting of a firstâ€² point in said second set; (h) identifying a second point in said first set having a weighting identical, within a predetermined tolerance, to the weighting of a secondâ€² point in said second set, wherein the distance between the first and second points in said first set is identical, within a predetermined tolerance, to the distance between the firstâ€² and secondâ€² points in said second set; (i) identifying a third point in said first set having a weighting identical, within a predetermined tolerance, to the weighting of a thirdâ€² point in said second set, wherein the distance between the first, second and third points in said first set is identical, within a predetermined tolerance, to the distance between the firstâ€², secondâ€² and thirdâ€² points in said second set; and (j) transforming the coordinates of one set of coordinate point so that the first, second, and third identified points of the first set coincide with the firstâ€², secondâ€², and thirdâ€² identified points of the second set within a predetermined tolerance to provide an alignment.