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dc.contributor.authorVreven, Thom
dc.contributor.authorHwang, Howook
dc.contributor.authorPierce, Brian G.
dc.contributor.authorWeng, Zhiping
dc.date2022-08-11T08:07:59.000
dc.date.accessioned2022-08-23T15:38:07Z
dc.date.available2022-08-23T15:38:07Z
dc.date.issued2012-03-01
dc.date.submitted2013-02-22
dc.identifier.citationProtein Sci. 2012 Mar;21(3):396-404. doi: 10.1002/pro.2027. Epub 2012 Feb 2. <a href="http://dx.doi.org/10.1002/pro.2027">Link to article on publisher's site</a>
dc.identifier.issn0961-8368 (Linking)
dc.identifier.doi10.1002/pro.2027
dc.identifier.pmid22238219
dc.identifier.urihttp://hdl.handle.net/20.500.14038/25867
dc.description.abstractWe present an energy function for predicting binding free energies of protein-protein complexes, using the three-dimensional structures of the complex and unbound proteins as input. Our function is a linear combination of nine terms and achieves a correlation coefficient of 0.63 with experimental measurements when tested on a benchmark of 144 complexes using leave-one-out cross validation. Although we systematically tested both atomic and residue-based scoring functions, the selected function is dominated by residue-based terms. Our function is stable for subsets of the benchmark stratified by experimental pH and extent of conformational change upon complex formation, with correlation coefficients ranging from 0.61 to 0.66.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=22238219&dopt=Abstract">Link to Article in PubMed</a>
dc.relation.urlhttp://dx.doi.org/10.1002/pro.2027
dc.subjectAlgorithms
dc.subjectAntigen-Antibody Complex
dc.subjectEntropy
dc.subject*Protein Binding
dc.subjectProtein Conformation
dc.subjectProteins
dc.subjectThermodynamics
dc.subjectBiochemistry, Biophysics, and Structural Biology
dc.subjectBioinformatics
dc.subjectComputational Biology
dc.subjectSystems Biology
dc.titlePrediction of protein-protein binding free energies
dc.typeJournal Article
dc.source.journaltitleProtein science : a publication of the Protein Society
dc.source.volume21
dc.source.issue3
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/bioinformatics_pubs/16
dc.identifier.contextkey3761397
html.description.abstract<p>We present an energy function for predicting binding free energies of protein-protein complexes, using the three-dimensional structures of the complex and unbound proteins as input. Our function is a linear combination of nine terms and achieves a correlation coefficient of 0.63 with experimental measurements when tested on a benchmark of 144 complexes using leave-one-out cross validation. Although we systematically tested both atomic and residue-based scoring functions, the selected function is dominated by residue-based terms. Our function is stable for subsets of the benchmark stratified by experimental pH and extent of conformational change upon complex formation, with correlation coefficients ranging from 0.61 to 0.66.</p>
dc.identifier.submissionpathbioinformatics_pubs/16
dc.contributor.departmentProgram in Bioinformatics and Integrative Biology
dc.contributor.departmentDepartment of Biochemistry and Molecular Pharmacology
dc.source.pages396-404


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