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.