Protein–protein docking: Progress in CAPRI rounds 6–12 using a combination of methods: The introduction of steered solvated molecular dynamics

Authors

  • Alexander Heifetz,

    1. Protein–Protein Interactions Group, Biosystems Informatics Institute, Marlborough House, Marlborough Crescent, Newcastle upon Tyne NE1 4EE, United Kingdom
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  • Sandeep Pal,

    Corresponding author
    1. Protein–Protein Interactions Group, Biosystems Informatics Institute, Marlborough House, Marlborough Crescent, Newcastle upon Tyne NE1 4EE, United Kingdom
    • Protein–Protein Interactions Group, Biosystems Informatics Institute, Marlborough House, Marlborough Crescent, Newcastle upon Tyne NE1 4EE, United Kingdom
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  • Graham R. Smith

    Corresponding author
    1. Protein–Protein Interactions Group, Biosystems Informatics Institute, Marlborough House, Marlborough Crescent, Newcastle upon Tyne NE1 4EE, United Kingdom
    • Protein–Protein Interactions Group, Biosystems Informatics Institute, Marlborough House, Marlborough Crescent, Newcastle upon Tyne NE1 4EE, United Kingdom
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Abstract

In recent rounds of CAPRI, the Bii group has employed a combination of techniques for the prediction of the structure of protein–protein complexes. We currently use third-party software for rigid-body and semiflexible docking (MolFit, 3D-Dock, RosettaDock), and our own steered molecular dynamics (SMD) technique for flexible refinement. SMD has also been found to be useful for discriminating near-native from false positive docking decoys. In addition to this, a variety of sources of information, including multiple descriptors of interface quality combined with a QSAR-like technique, published biological information, and continuum electrostatics calculations, are also used in the assessment of candidate complexes. We shall concentrate on results for CAPRI rounds 9–11 (targets 24–27). In these rounds, the Bii group has been successful in submitting a medium quality model for each of CAPRI targets 25 and 26, and a model of acceptable quality for target 27. Proteins 2007. © 2007 Wiley-Liss, Inc.

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