title: 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 the monomer alignment program of TM-align, the alignment accuracy of MM-align is significantly higher as judged by the average TM-score of the physically-aligned residues. MM-align is about two times faster than TM-align because of omitting the cross-alignment zone of the DP matrix. It also shows that the enhanced alignment of the interfaces helps in identifying biologically relevant protein complex pairs.
authors.affiliation: Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 66047, USA.
authors.forename: Srayanta
authors.initials: S
authors.lastname: Mukherjee
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry*; D025941:Protein Interaction Mapping / Q000379:methods*; D020836:Protein Structure, Quaternary; D016415:Sequence Alignment
chemical_list: D046912:Multiprotein Complexes