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
JournalProteins
Volume60
Issue2
Pagination214-6
Date Published2005 Aug 1
ISSN1097-0134
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
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.

DOI10.1002/prot.20560
Alternate JournalProteins
PubMed ID15981264