MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming.

ABSTRACT: Structural comparison of multiple-chain protein complexes is essential in many studies of protein-protein interactions. We develop a new algorithm, MM-align, for sequence-independent alignment of protein complex structures. The algorithm is built on a heuristic iteration of a modified Needleman-Wunsch dynamic programming (DP) algorithm, with the alignment score specified by the inter-complex residue distances. The multiple chains in each complex are first joined, in every possible order, and then simultaneously aligned with cross-chain alignments prevented. The alignments of interface residues are enhanced by an interface-specific weighting factor. MM-align is tested on a large-scale benchmark set of 205 x 3897 non-homologous multiple-chain complex pairs. Compared with a naïve extension of

SUBMITTER: Mukherjee S 

PROVIDER: S-EPMC2699532 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature