26 lines
1.4 KiB
XML
26 lines
1.4 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
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<pkgmetadata>
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<maintainer type="project">
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<email>sci-chemistry@gentoo.org</email>
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<name>Gentoo Chemistry Project</name>
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</maintainer>
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<longdescription>
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MM-align is an algorithm for structurally aligning multiple-chain
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protein-protein complexes. The algorithm is built on a heuristic
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iteration of a modified Needleman-Wunsch dynamic programming (DP)
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algorithm, with the alignment score specified by the inter-complex residue
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distances. The multiple chains in each complex are first joined, in every
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possible order, and then simultaneously aligned with cross-chain alignments
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prevented. The alignments of interface residues are enhanced by an
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interface-specific weighting factor. An optimal alignment between two complexes,
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as well as the overall TM-score, will be reported for each comparison.
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What is the difference between TM-align and MM-align? TM-align is for aligning
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monomer protein structures while MM-align is designed for aligning
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multiple-chain protein complex structures. Although one can still use TM-align
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to align protein complexes after manually joining the chains, this will lead
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to suboptimal alignments with unphysical cross alignments. Therefore, the
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best result will be obtained if one uses TM-align to monomer structures and
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MM-align for multimer structures.
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</longdescription>
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</pkgmetadata>
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