Show simple item record

dc.contributor.authorVreven, Thom
dc.contributor.authorHwang, Howook
dc.contributor.authorWeng, Zhiping
dc.date2022-08-11T08:07:59.000
dc.date.accessioned2022-08-23T15:38:10Z
dc.date.available2022-08-23T15:38:10Z
dc.date.issued2011-09-01
dc.date.submitted2013-02-22
dc.identifier.citation<p>Protein Sci. 2011 Sep;20(9):1576-86. doi: 10.1002/pro.687. Epub 2011 Aug 8. <a href="http://dx.doi.org/10.1002/pro.687">Link to article on publisher's site</a></p>
dc.identifier.issn0961-8368 (Linking)
dc.identifier.doi10.1002/pro.687
dc.identifier.pmid21739500
dc.identifier.urihttp://hdl.handle.net/20.500.14038/25881
dc.description.abstractMost scoring functions for protein-protein docking algorithms are either atom-based or residue-based, with the former being able to produce higher quality structures and latter more tolerant to conformational changes upon binding. Earlier, we developed the ZRANK algorithm for reranking docking predictions, with a scoring function that contained only atom-based terms. Here we combine ZRANK's atom-based potentials with five residue-based potentials published by other labs, as well as an atom-based potential IFACE that we published after ZRANK. We simultaneously optimized the weights for selected combinations of terms in the scoring function, using decoys generated with the protein-protein docking algorithm ZDOCK. We performed rigorous cross validation of the combinations using 96 test cases from a docking benchmark. Judged by the integrative success rate of making 1000 predictions per complex, addition of IFACE and the best residue-based pair potential reduced the number of cases without a correct prediction by 38 and 27% relative to ZDOCK and ZRANK, respectively. Thus combination of residue-based and atom-based potentials into a scoring function can improve performance for protein-protein docking. The resulting scoring function is called IRAD (integration of residue- and atom-based potentials for docking) and is available at http://zlab.umassmed.edu.
dc.language.isoen_US
dc.relation<p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=21739500&dopt=Abstract">Link to Article in PubMed</a></p>
dc.relation.urlhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3190152/
dc.subjectAlgorithms
dc.subjectProtein Binding
dc.subjectProtein Conformation
dc.subjectProteins
dc.subjectAmino Acids, Peptides, and Proteins
dc.subjectBioinformatics
dc.subjectComputational Biology
dc.subjectSystems Biology
dc.titleIntegrating atom-based and residue-based scoring functions for protein-protein docking
dc.typeArticle
dc.source.journaltitleProtein science : a publication of the Protein Society
dc.source.volume20
dc.source.issue9
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/bioinformatics_pubs/23
dc.identifier.contextkey3761404
html.description.abstract<p>Most scoring functions for protein-protein docking algorithms are either atom-based or residue-based, with the former being able to produce higher quality structures and latter more tolerant to conformational changes upon binding. Earlier, we developed the ZRANK algorithm for reranking docking predictions, with a scoring function that contained only atom-based terms. Here we combine ZRANK's atom-based potentials with five residue-based potentials published by other labs, as well as an atom-based potential IFACE that we published after ZRANK. We simultaneously optimized the weights for selected combinations of terms in the scoring function, using decoys generated with the protein-protein docking algorithm ZDOCK. We performed rigorous cross validation of the combinations using 96 test cases from a docking benchmark. Judged by the integrative success rate of making 1000 predictions per complex, addition of IFACE and the best residue-based pair potential reduced the number of cases without a correct prediction by 38 and 27% relative to ZDOCK and ZRANK, respectively. Thus combination of residue-based and atom-based potentials into a scoring function can improve performance for protein-protein docking. The resulting scoring function is called IRAD (integration of residue- and atom-based potentials for docking) and is available at http://zlab.umassmed.edu.</p>
dc.identifier.submissionpathbioinformatics_pubs/23
dc.contributor.departmentProgram in Bioinformatics and Integrative Biology
dc.contributor.departmentDepartment of Biochemistry and Molecular Pharmacology
dc.source.pages1576-86


This item appears in the following Collection(s)

Show simple item record