title: Protein-protein docking benchmark version 4.0.
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/.
authors.affiliation: Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
authors.forename: Howook
authors.initials: H
authors.lastname: Hwang
authors.forename: Thom
authors.initials: T
authors.lastname: Vreven
authors.forename: Joël
authors.initials: J
authors.lastname: Janin
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D008956:Models, Chemical; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012984:Software
chemical_list: D011506:Proteins
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