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dc.contributor.authorBohnuud, Tanggis
dc.contributor.authorLuo, Lingqi
dc.contributor.authorWodak, Shoshana J.
dc.contributor.authorBonvin, Alexandre M. J. J.
dc.contributor.authorWeng, Zhiping
dc.contributor.authorVajda, Sandor
dc.contributor.authorSchueler-Furman, Ora
dc.contributor.authorKozakov, Dima
dc.date2022-08-11T08:07:59.000
dc.date.accessioned2022-08-23T15:38:29Z
dc.date.available2022-08-23T15:38:29Z
dc.date.issued2016-05-12
dc.date.submitted2016-07-22
dc.identifier.citationProteins. 2016 May 12. doi: 10.1002/prot.25063. <a href="http://dx.doi.org/10.1002/prot.25063">Link to article on publisher's site</a>
dc.identifier.issn0887-3585 (Linking)
dc.identifier.doi10.1002/prot.25063
dc.identifier.pmid27172383
dc.identifier.urihttp://hdl.handle.net/20.500.14038/25944
dc.description.abstractProtein docking procedures carry out the task of predicting the structure of a protein-protein complex starting from the known structures of the individual protein components. More often than not, however, the structure of one or both components is not known, but can be derived by homology modeling on the basis of known structures of related proteins deposited in the Protein Data Bank (PDB). Thus, the problem is to develop methods that optimally integrate homology modeling and docking with the goal of predicting the structure of a complex directly from the amino acid sequences of its component proteins. One possibility is to use the best available homology modeling and docking methods. However, the models built for the individual subunits often differ to a significant degree from the bound conformation in the complex, often much more so than the differences observed between free and bound structures of the same protein, and therefore additional conformational adjustments, both at the backbone and side chain levels need to be modeled to achieve an accurate docking prediction. In particular, even homology models of overall good accuracy frequently include localized errors that unfavorably impact docking results. The predicted reliability of the different regions in the model can also serve as a useful input for the docking calculations. Here we present a benchmark dataset that should help to explore and solve combined modeling and docking problems. This dataset comprises a subset of the experimentally solved 'target' complexes from the widely used Docking Benchmark from the Weng Lab (excluding antibody-antigen complexes). This subset is extended to include the structures from the PDB related to those of the individual components of each complex, and hence represent potential templates for investigating and benchmarking integrated homology modeling and docking approaches. Template sets can be dynamically customized by specifying ranges in sequence similarity and in PDB release dates, or using other filtering options, such as excluding sets of specific structures from the template list. Multiple sequence alignments, as well as structural alignments of the templates to their corresponding subunits in the target are also provided. The resource is accessible online or can be downloaded at http://cluspro.org/benchmark, and is updated on a weekly basis in synchrony with new PDB releases.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=27172383&dopt=Abstract">Link to Article in PubMed</a>
dc.relation.urlhttp://dx.doi.org/10.1002/prot.25063
dc.subjectCAPRI docking experiment
dc.subjectmethod development
dc.subjectprotein structure prediction
dc.subjectprotein-protein docking
dc.subjectuser community
dc.subjectBioinformatics
dc.subjectComputational Biology
dc.subjectIntegrative Biology
dc.subjectStructural Biology
dc.titleA benchmark testing ground for integrating homology modeling and protein docking
dc.typeArticle
dc.source.journaltitleProteins
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/bioinformatics_pubs/84
dc.identifier.contextkey8870393
html.description.abstract<p>Protein docking procedures carry out the task of predicting the structure of a protein-protein complex starting from the known structures of the individual protein components. More often than not, however, the structure of one or both components is not known, but can be derived by homology modeling on the basis of known structures of related proteins deposited in the Protein Data Bank (PDB). Thus, the problem is to develop methods that optimally integrate homology modeling and docking with the goal of predicting the structure of a complex directly from the amino acid sequences of its component proteins. One possibility is to use the best available homology modeling and docking methods. However, the models built for the individual subunits often differ to a significant degree from the bound conformation in the complex, often much more so than the differences observed between free and bound structures of the same protein, and therefore additional conformational adjustments, both at the backbone and side chain levels need to be modeled to achieve an accurate docking prediction. In particular, even homology models of overall good accuracy frequently include localized errors that unfavorably impact docking results. The predicted reliability of the different regions in the model can also serve as a useful input for the docking calculations. Here we present a benchmark dataset that should help to explore and solve combined modeling and docking problems. This dataset comprises a subset of the experimentally solved 'target' complexes from the widely used Docking Benchmark from the Weng Lab (excluding antibody-antigen complexes). This subset is extended to include the structures from the PDB related to those of the individual components of each complex, and hence represent potential templates for investigating and benchmarking integrated homology modeling and docking approaches. Template sets can be dynamically customized by specifying ranges in sequence similarity and in PDB release dates, or using other filtering options, such as excluding sets of specific structures from the template list. Multiple sequence alignments, as well as structural alignments of the templates to their corresponding subunits in the target are also provided. The resource is accessible online or can be downloaded at http://cluspro.org/benchmark, and is updated on a weekly basis in synchrony with new PDB releases.</p>
dc.identifier.submissionpathbioinformatics_pubs/84
dc.contributor.departmentProgram in Bioinformatics and Integrative Biology


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