MM-align is an algorithm for structurally aligning multiple-chain protein-protein complexes. 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.
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S. Mukherjee, Y. Zhang,
MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming.
Nucleic Acids Research 2009; 37: e83