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MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming
dc.contributor.author | Mukherjee, Srayanta | |
dc.contributor.author | Zhang, Yang | |
dc.date.accessioned | 2014-04-15T21:48:21Z | |
dc.date.available | 2014-04-15T21:48:21Z | |
dc.date.issued | 2009-05-14 | |
dc.identifier.citation | Mukherjee, Sourav, Alicia M Hanson, William R Shadrick, Jean Ndjomou, Noreena L Sweeney, John J Hernandez, Diana Bartczak, et al. 2012. “Identification and Analysis of Hepatitis C Virus NS3 Helicase Inhibitors Using Nucleic Acid Binding Assays.” Nucleic Acids Research 40 (17): 8607–21. http://dx.doi.org/10.1093/nar/gks623 | |
dc.identifier.uri | http://hdl.handle.net/1808/13523 | |
dc.description.abstract | Structural comparison of multiple-chain protein complexes is essential in many studies of protein–protein interactions. We develop a new algorithm, MM-align, for sequence-independent alignment of protein complex structures. 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. MM-align is tested on a large-scale benchmark set of 205 × 3897 non-homologous multiple-chain complex pairs. Compared with a naïve extension of the monomer alignment program of TM-align, the alignment accuracy of MM-align is significantly higher as judged by the average TM-score of the physically-aligned residues. MM-align is about two times faster than TM-align because of omitting the cross-alignment zone of the DP matrix. It also shows that the enhanced alignment of the interfaces helps in identifying biologically relevant protein complex pairs. | |
dc.description.sponsorship | Alfred P. Sloan Foundation; NSF Career Award (DBI 0746198); and the National Institute of General Medical Sciences (R01GM083107, R01GM084222). Funding for open access charge: Alfred P. Sloan Research Fellowship. | |
dc.publisher | MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming | |
dc.rights | 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. | |
dc.rights.uri | http://creativecommons.org/licenses/by-nc/2.0/uk/ | |
dc.title | MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming | |
dc.type | Article | |
kusw.kuauthor | Mukherjee, Srayanta | |
kusw.kuauthor | Zhang, Yang | |
kusw.kudepartment | Department of Molecular Biosciences | |
kusw.oastatus | fullparticipation | |
dc.identifier.doi | 10.1093/nar/gkp318 | |
kusw.oaversion | Scholarly/refereed, publisher version | |
kusw.oapolicy | This item meets KU Open Access policy criteria. | |
dc.rights.accessrights | openAccess |
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Except where otherwise noted, this item's license is described as: 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.