Finding sub-graphs from contact map overlap problem

Abstract

Protein structure comparison is one of the most challenging problem 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 in this area. Protein contact map is a two dimensional representation of protein tertiary structure. The goal of this work is to find frequent sub-graphs from contact maps. We propose a simple and computationally inexpensive algorithm is depth first search approach to contact map overlap problem for finding sub graphs from whole contact map of each protein structure. The sub-graph approach is evaluating on two bench mark data sets are SOKOL and SKOLNICK. It is interesting to note that along with achieving better sub-graphs is also obtained for certain protein folds. Further these sub graphs are used successfully in addressing the problem of protein fold classification.