Incorporation of flexibility into rigid-body docking: Applications in rounds 3–5 of CAPRI

Authors

  • Graham R. Smith,

    1. Biomolecular Modelling Laboratory, Cancer Research U.K. London Research Institute, Lincoln's Inn Fields Laboratories, London, United Kingdom
    Current affiliation:
    1. Biosystems Informatics Institute, International Centre for Life, Newcastle upon Tyne, NE1 4EP, UK
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  • Paul W. Fitzjohn,

    1. Biomolecular Modelling Laboratory, Cancer Research U.K. London Research Institute, Lincoln's Inn Fields Laboratories, London, United Kingdom
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  • Christopher S. Page,

    1. Biomolecular Modelling Laboratory, Cancer Research U.K. London Research Institute, Lincoln's Inn Fields Laboratories, London, United Kingdom
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  • Paul A. Bates

    Corresponding author
    1. Biomolecular Modelling Laboratory, Cancer Research U.K. London Research Institute, Lincoln's Inn Fields Laboratories, London, United Kingdom
    • Biomolecular Modelling Laboratory, Cancer Research U.K. London Research Institute, Lincoln's Inn Field Laboratories, 44 Lincoln's Inn Fields, London WC2A 3PX, UK
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Abstract

We have submitted models for all 9 targets in Rounds 3–5 of CAPRI and have predicted at least 30% of the correct contacts for 4 of the targets and at least 10% of the correct contacts for another 4 targets. We have employed a variety of techniques but have had the greatest success by combining established rigid-body docking with a variety of initial conformations generated by molecular dynamics. Proteins 2005;60:263–268. © 2005 Wiley-Liss, Inc.

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