Protein–protein docking benchmark version 4.0

Authors

  • Howook Hwang,

    1. Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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  • Thom Vreven,

    1. Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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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. Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
    • Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Room 1010, Lazare Research Building, 364 Plantation St, Worcester, MA 01605
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  • The authors state no conflict of interest.

Abstract

We updated our protein–protein docking benchmark to include complexes that became available since our previous release. As before, we only considered high-resolution complex structures that are nonredundant at the family–family pair level, for which the X-ray or NMR unbound structures of the constituent proteins are also available. Benchmark 4.0 adds 52 new complexes to the 124 cases of Benchmark 3.0, representing an increase of 42%. Thus, benchmark 4.0 provides 176 unbound–unbound cases that can be used for protein–protein docking method development and assessment. Seventeen of the newly added cases are enzyme-inhibitor complexes, and we found no new antigen-antibody complexes. Classifying the new cases according to expected difficulty for protein–protein docking algorithms gives 33 rigid body cases, 11 cases of medium difficulty, and 8 cases that are difficult. Benchmark 4.0 listings and processed structure files are publicly accessible at http://zlab.umassmed.edu/benchmark/ Proteins 2010. © 2010 Wiley-Liss, Inc.

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