| <?xml version="1.0" encoding="UTF-8"?> |
| <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| <pkgmetadata> |
| <herd>sci-chemistry</herd> |
| <maintainer> |
| <email>jlec@gentoo.org</email> |
| </maintainer> |
| <longdescription> |
| 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. |
| </longdescription> |
| </pkgmetadata> |
