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dc.contributor.authorPulim, Vinayen_US
dc.contributor.authorBerger, Bonnieen_US
dc.contributor.authorBienkowska, Jadwigaen_US
dc.date.accessioned2012-01-11T00:37:41Z
dc.date.available2012-01-11T00:37:41Z
dc.date.copyright2008en_US
dc.date.issued2008-8-18en_US
dc.identifier.citationPulim, Vinay, Bonnie Berger, Jadwiga Bienkowska. "Optimal contact map alignment of protein–protein interfaces" Bioinformatics 24(20): 2324-2328. (2008)en_US
dc.identifier.issn1460-2059en_US
dc.identifier.urihttps://hdl.handle.net/2144/3009
dc.description.abstractThe long-standing problem of constructing protein structure alignments is of central importance in computational biology. The main goal is to provide an alignment of residue correspondences, in order to identify homologous residues across chains. A critical next step of this is the alignment of protein complexes and their interfaces. Here, we introduce the program CMAPi, a two-dimensional dynamic programming algorithm that, given a pair of protein complexes, optimally aligns the contact maps of their interfaces: it produces polynomial-time near-optimal alignments in the case of multiple complexes. We demonstrate the efficacy of our algorithm on complexes from PPI families listed in the SCOPPI database and from highly divergent cytokine families. In comparison to existing techniques, CMAPi generates more accurate alignments of interacting residues within families of interacting proteins, especially for sequences with low similarity. While previous methods that use an all-atom based representation of the interface have been successful, CMAPi's use of a contact map representation allows it to be more tolerant to conformational changes and thus to align more of the interaction surface. These improved interface alignments should enhance homology modeling and threading methods for predicting PPIs by providing a basis for generating template profiles for sequence–structure alignment. Contact: bab@mit.edu; jbienkowska@gmail.com Supplementary information: Supplementary data are available at http://theory.csail.mit.edu/cmapien_US
dc.description.sponsorshipNational Institute of Health (1R01GM081871-01A1)en_US
dc.language.isoenen_US
dc.publisherOxford University Pressen_US
dc.rightsCopyright 2008 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.en_US
dc.rights.urihttp://creativecommons.org/licenses/by-nc/2.0/uk/en_US
dc.titleOptimal Contact Map Alignment of Protein–Protein Interfacesen_US
dc.typeArticleen_US
dc.identifier.doi10.1093/bioinformatics/btn432en_US
dc.identifier.pmid18710876en_US
dc.identifier.pmcid2562013en_US


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Copyright 2008 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Except where otherwise noted, this item's license is described as Copyright 2008 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.