Joining Softassign and Dynamic Programming for the Contact Map Overlap Problem

Comparison of 3-dimensional protein folds is a core problem in molecular biology. The Contact Map Overlap (CMO) scheme provides one of the most common measures for protein structure similarity. Maximizing CMO is, however, NP-hard. To approximately solve CMO, we combine softassign and dynamic programming. Softassign approximately solves the maximum common subgraph (MCS) problem. Dynamic programming converts the MCS solution to a solution of the CMO problem. We present and discuss experiments using proteins with up to 1500 residues. The results indicate that the proposed method is extremely fast compared to other methods, scales well with increasing problem size, and is useful for comparing similar protein structures.