Protein-protein docking benchmark version 4.0
| dc.contributor.author | Hwang, Howook | |
| dc.contributor.author | Vreven, Thom | |
| dc.contributor.author | Janin, Joel | |
| dc.contributor.author | Weng, Zhiping | |
| dc.date | 2022-08-11T08:07:59.000 | |
| dc.date.accessioned | 2022-08-23T15:38:13Z | |
| dc.date.available | 2022-08-23T15:38:13Z | |
| dc.date.issued | 2010-11-15 | |
| dc.date.submitted | 2013-02-22 | |
| dc.identifier.citation | <p>Proteins. 2010 Nov 15;78(15):3111-4. doi: 10.1002/prot.22830. <a href="http://dx.doi.org/10.1002/prot.22830">Link to article on publisher's site</a></p> | |
| dc.identifier.issn | 0887-3585 (Linking) | |
| dc.identifier.doi | 10.1002/prot.22830 | |
| dc.identifier.pmid | 20806234 | |
| dc.identifier.uri | http://hdl.handle.net/20.500.14038/25889 | |
| dc.description.abstract | We updated our protein-protein docking benchmark to include complexes that became available since our previous release. As before, we only considered high-resolution complex structures that are nonredundant at the family-family pair level, for which the X-ray or NMR unbound structures of the constituent proteins are also available. Benchmark 4.0 adds 52 new complexes to the 124 cases of Benchmark 3.0, representing an increase of 42%. Thus, benchmark 4.0 provides 176 unbound-unbound cases that can be used for protein-protein docking method development and assessment. Seventeen of the newly added cases are enzyme-inhibitor complexes, and we found no new antigen-antibody complexes. Classifying the new cases according to expected difficulty for protein-protein docking algorithms gives 33 rigid body cases, 11 cases of medium difficulty, and 8 cases that are difficult. Benchmark 4.0 listings and processed structure files are publicly accessible at http://zlab.umassmed.edu/benchmark/. | |
| dc.language.iso | en_US | |
| dc.relation | <p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=20806234&dopt=Abstract">Link to Article in PubMed</a></p> | |
| dc.relation.url | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958056/ | |
| dc.subject | *Algorithms | |
| dc.subject | Computational Biology | |
| dc.subject | Crystallography, X-Ray | |
| dc.subject | Databases, Protein | |
| dc.subject | *Models, Chemical | |
| dc.subject | Models, Molecular | |
| dc.subject | Nuclear Magnetic Resonance, Biomolecular | |
| dc.subject | Protein Conformation | |
| dc.subject | Protein Interaction Mapping | |
| dc.subject | Proteins | |
| dc.subject | *Software | |
| dc.subject | protein-protein docking | |
| dc.subject | protein complexes | |
| dc.subject | protein-protein interactions | |
| dc.subject | complex structure | |
| dc.subject | Amino Acids, Peptides, and Proteins | |
| dc.subject | Biochemistry, Biophysics, and Structural Biology | |
| dc.subject | Bioinformatics | |
| dc.subject | Computational Biology | |
| dc.subject | Systems Biology | |
| dc.title | Protein-protein docking benchmark version 4.0 | |
| dc.type | Journal Article | |
| dc.source.journaltitle | Proteins | |
| dc.source.volume | 78 | |
| dc.source.issue | 15 | |
| dc.identifier.legacycoverpage | https://escholarship.umassmed.edu/bioinformatics_pubs/30 | |
| dc.identifier.contextkey | 3761411 | |
| html.description.abstract | <p>We updated our protein-protein docking benchmark to include complexes that became available since our previous release. As before, we only considered high-resolution complex structures that are nonredundant at the family-family pair level, for which the X-ray or NMR unbound structures of the constituent proteins are also available. Benchmark 4.0 adds 52 new complexes to the 124 cases of Benchmark 3.0, representing an increase of 42%. Thus, benchmark 4.0 provides 176 unbound-unbound cases that can be used for protein-protein docking method development and assessment. Seventeen of the newly added cases are enzyme-inhibitor complexes, and we found no new antigen-antibody complexes. Classifying the new cases according to expected difficulty for protein-protein docking algorithms gives 33 rigid body cases, 11 cases of medium difficulty, and 8 cases that are difficult. Benchmark 4.0 listings and processed structure files are publicly accessible at http://zlab.umassmed.edu/benchmark/.</p> | |
| dc.identifier.submissionpath | bioinformatics_pubs/30 | |
| dc.contributor.department | Program in Bioinformatics and Integrative Biology | |
| dc.contributor.department | Department of Biochemistry and Molecular Pharmacology | |
| dc.source.pages | 3111-4 |
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