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Protein-Protein Docking Benchmark 2.0: an update.

Julian Mintseris·Kevin Wiehe·Brian Pierce·Robert Anderson·Rong Chen·Joël Janin·Zhiping Weng
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Abstract

We present a new version of the Protein-Protein Docking Benchmark, reconstructed from the bottom up to include more complexes, particularly focusing on more unbound-unbound test cases. SCOP (Structural Classification of Proteins) was used to assess redundancy between the complexes in this version. The new benchmark consists of 72 unbound-unbound cases, with 52 rigid-body cases, 13 medium-difficulty cases, and 7 high-difficulty cases with substantial conformational change. In addition, we retained 12 antibody-antigen test cases with the antibody structure in the bound form. The new benchmark provides a platform for evaluating the progress of docking methods on a wide variety of targets. The new version of the benchmark is available to the public at http://zlab.bu.edu/benchmark2.

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AlgorithmsAnimalsAutomationComputational BiologyComputer SimulationCrystallography, X-RayDatabases, ProteinDimerizationHumansInternetMacromolecular SubstancesModels, MolecularModels, StatisticalMolecular ConformationProtein BindingProtein ConformationProtein FoldingProtein Interaction MappingProtein Structure, TertiaryProteomicsReproducibility of ResultsSoftwareStructural Homology, ProteinJournal ArticleResearch Support, U.S. Gov't, Non-P.H.S.

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Julian Mintseris, Kevin Wiehe, Brian Pierce, Robert Anderson, Rong Chen, Joël Janin, Zhiping Weng. 2005-08-01. Protein-Protein Docking Benchmark 2.0: an update.. https://doi.org/10.1002/prot.20560

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