Protein-Protein Docking Benchmark 2.0: an update.

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TitleProtein-Protein Docking Benchmark 2.0: an update.
Publication TypeJournal Article
Year of Publication2005
AuthorsMintseris, J, Wiehe, K, Pierce, BG, Anderson, R, Chen, R, Janin, J, Weng, Z
Date Published2005 Aug 1
KeywordsAlgorithms, Animals, Automation, Computational Biology, Computer Simulation, Crystallography, X-Ray, Databases, Protein, Dimerization, Humans, Internet, Macromolecular Substances, Models, Molecular, Models, Statistical, Molecular Conformation, Protein Binding, Protein Conformation, Protein Folding, Protein Interaction Mapping, Protein Structure, Tertiary, Proteomics, Reproducibility of Results, Software, Structural Homology, Protein

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

Alternate JournalProteins
PubMed ID15981264