Patent ID: 8452542
Filing Date: 2013-05-28
Classification: G16B

Abstract:
1. A computer-implemented method of scoring a set of residues within a cluster of proteins from an initial set of three dimensional protein structures, comprising: identifying, by a computer, the initial set of three dimensional protein structures, each comprising a polypeptide sequence and structural coordinates; generating, by the computer, a plurality of pair-wise protein structure alignments of the set of three dimensional protein structures; for each pair of protein structures in the set: generating, by the computer, a cluster of protein structures from the initial set of protein structures using the identified pair-wise candidate spans, the pair-wise local similarity values, and the pair-wise global similarity values; aligning, by the computer, all protein structures in the cluster to generate a one-to-one residue correspondence of the residue pairs for the cluster of protein structures; identifying, by the computer, a span from the cluster of protein structures, wherein each span comprises a set of one-to-one correspondences of residues that are within the first pre-determined distance of each other and within the second pre-determined distance based on the plurality of pair-wise structural alignments of the cluster of protein structures; generating, by the computer, a plurality of conservation scores for the cluster of protein structures, wherein the conservation scores are calculated for a plurality of residues within the span based on a metric for residue similarity; and storing, by the computer, the plurality of conservation scores, thereby scoring the set of residues within the cluster of protein structures.