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Nucleic Acids Research Advance Access originally published online on May 14, 2009
Nucleic Acids Research 2009 37(11):e83; doi:10.1093/nar/gkp318
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Nucleic Acids Research, 2009, Vol. 37, No. 11 e83
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

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

Srayanta Mukherjee and Yang Zhang*

Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 66047, USA

*To whom correspondence should be addressed. Tel: +1 785 864 1963; Fax: 001-785-864-5558; Email: yzhang{at}ku.edu

Received December 24, 2008. Accepted April 17, 2009.

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.


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