Protein structure similarity using recurrence relation technique

Abstract

Protein structure comparison is one of the most challenging problems in Bioinformatics. This problem is modeled as a contact map overlap problem in which the similarity of the two proteins being compared is measured by the amount of ‘overlap’ between their corresponding protein contact maps. To find a maximum overlap is proved to be an NP-hard problem [8]. Many heuristics have been proposed for contact map overlap(CMO) problem, which achieve excellent performance on bench-mark data sets. We propose a new eight neighbor algorithm for extraction of regions from contact maps. We propose to build a recurrence relation technique to address protein structure comparison via contact map overlap problem. Using exact region matching algorithm we find a matching region in the other contact map, then use one heuristics internally between each pair of matched regions to construct an alignment. If two proteins are similar, we can align the corresponding 2D-clusters such that the contact map overlap problem be addressed on the basis of these ‘matching’ clusters. Finally we merge the region-wise alignments. An obvious advantage of this algorithm is that it facilitates parallel processing technique.