Bimal: Bipartite matching alignment for the contact map overlap problem

Bimal, a fast method for approximately solving the maximum contact map overlap (maxCMO) problem is introduced. The method is based on an approximate model of the maxCMO-problem using the generic bipartite graph matching framework, which is then optimally solved by double dynamic programming. The performance of Bimal has been evaluated in an empirical comparative study including clustering of protein structures according to the SCOP fold´s level. Solving about 800 pairwise alignments of medium-sized proteins takes less than 1 min on a 1.7 GHz machine and yields good results for similar protein structures. Bimal accurately classified proteins in agreement with the SCOP classification. In particular, for similar proteins, Bimal provides a good tradeoff between computation speed and solution quality and is because of its high speed useful for solving large-scaled maxCMO applications.