sci-chemistry jlec@gentoo.org 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. An optimal alignment between two complexes, as well as the overall TM-score, will be reported for each comparison. What is the difference between TM-align and MM-align? TM-align is for aligning monomer protein structures while MM-align is designed for aligning multiple-chain protein complex structures. Although one can still use TM-align to align protein complexes after manually joining the chains, this will lead to suboptimal alignments with unphysical cross alignments. Therefore, the best result will be obtained if one uses TM-align to monomer structures and MM-align for multimer structures.