Protein-protein docking benchmark version 3.0
Department of Biochemistry and Molecular Pharmacology; Program in Bioinformatics and Integrative Biology
Medical Subject Headings
*Algorithms; Animals; Databases, Protein; Internet; Protein Interaction Mapping
Bioinformatics | Computational Biology | Systems Biology
We present version 3.0 of our publicly available protein-protein docking benchmark. This update includes 40 new test cases, representing a 48% increase from Benchmark 2.0. For all of the new cases, the crystal structures of both binding partners are available. As with Benchmark 2.0, Structural Classification of Proteins (Murzin et al., J Mol Biol 1995;247:536-540) was used to remove redundant test cases. The 124 unbound-unbound test cases in Benchmark 3.0 are classified into 88 rigid-body cases, 19 medium-difficulty cases, and 17 difficult cases, based on the degree of conformational change at the interface upon complex formation. In addition to providing the community with more test cases for evaluating docking methods, the expansion of Benchmark 3.0 will facilitate the development of new algorithms that require a large number of training examples. Benchmark 3.0 is available to the public at http://zlab.bu.edu/benchmark.
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Citation: Proteins. 2008 Nov 15;73(3):705-9. doi: 10.1002/prot.22106. Link to article on publisher's site
Hwang, Howook; Pierce, Brian G.; Mintseris, Julian; Janin, Joel; and Weng, Zhiping, "Protein-protein docking benchmark version 3.0" (2008). Program in Bioinformatics and Integrative Biology Publications and Presentations. Paper 42.