sci-chemistry / mm-align

Protein Complex Structural Alignment

Official package sites : http://zhanglab.ccmb.med.umich.edu/MM-align/ ·

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.

v20120321 :: 0 :: gentoo

Modified
License
tm-align
Keywords
~amd64 ~amd64-linux ~x86 ~x86-linux

dev-util / cmake : Cross platform Make

sys-devel / make : Standard tool to compile source trees

virtual / fortran : Virtual for Fortran Compiler

virtual / fortran : Virtual for Fortran Compiler

sci-chemistry / pymol-plugins-psico : Pymol ScrIpt COllection

Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
Johannes Huber · gentoo
sci-chemistry/mm-align: EAPI 6
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Justin Lecher · gentoo
Use https by default
Convert all URLs for sites supporting encrypted connections from http to https Signed-off-by: Justin Lecher <jlec@gentoo.org>
Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed