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Protein–protein docking benchmark version 3.0

Authors

  • Howook Hwang,

    1. Bioinformatics Program, Boston University, Boston, Massachusetts 02215
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  • Brian Pierce,

    1. Bioinformatics Program, Boston University, Boston, Massachusetts 02215
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  • Julian Mintseris,

    1. Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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  • Joël Janin,

    1. Yeast Structural Genomics, IBBMC Université Paris-Sud, CNRS UMR 8619, 91405-Orsay, France
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  • Zhiping Weng

    Corresponding author
    1. Bioinformatics Program, Boston University, Boston, Massachusetts 02215
    2. Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215
    3. Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
    • Program in Bioinformatics and Integrative Biology, The University of Massachusetts Medical School, Room 1010, Lazare Research Building, 364 Plantation St., Worcester, MA 01605
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Abstract

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. Proteins 2008. © 2008 Wiley-Liss, Inc.

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