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HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets

Authors

  • Sjoerd J. de Vries,

    1. Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, 3584CH, Utrecht, The Netherlands
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  • Aalt D. J. van Dijk,

    1. Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, 3584CH, Utrecht, The Netherlands
    Current affiliation:
    1. Applied Bioinformatics, Plant Research International, Wageningen UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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  • Mickaël Krzeminski,

    1. Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, 3584CH, Utrecht, The Netherlands
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  • Mark van Dijk,

    1. Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, 3584CH, Utrecht, The Netherlands
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  • Aurelien Thureau,

    1. Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, 3584CH, Utrecht, The Netherlands
    Current affiliation:
    1. CNRS, ICSN, Laboratoire de Chimie et Biologie Structurales, 1 avenue de la terrasse, 91190, Gif-sur-Yvette, France
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  • Victor Hsu,

    1. Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305
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  • Tsjerk Wassenaar,

    1. Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, 3584CH, Utrecht, The Netherlands
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  • Alexandre M. J. J. Bonvin

    Corresponding author
    1. Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, 3584CH, Utrecht, The Netherlands
    • Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, 3584CH, Utrecht, The Netherlands
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Abstract

Here we present version 2.0 of HADDOCK, which incorporates considerable improvements and new features. HADDOCK is now able to model not only protein–protein complexes but also other kinds of biomolecular complexes and multi-component (N > 2) systems. In the absence of any experimental and/or predicted information to drive the docking, HADDOCK now offers two additional ab initio docking modes based on either random patch definition or center-of-mass restraints. The docking protocol has been considerably improved, supporting among other solvated docking, automatic definition of semi-flexible regions, and inclusion of a desolvation energy term in the scoring scheme. The performance of HADDOCK2.0 is evaluated on the targets of rounds 4-11, run in a semi-automated mode using the original information we used in our CAPRI submissions. This enables a direct assessment of the progress made since the previous versions. Although HADDOCK performed very well in CAPRI (65% and 71% success rates, overall and for unbound targets only, respectively), a substantial improvement was achieved with HADDOCK2.0. Proteins 2007. © 2007 Wiley-Liss, Inc.

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