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Solvated protein–protein docking using Kyte-Doolittle-based water preferences

Authors

  • Panagiotis L. Kastritis,

    1. Bijvoet Center for Biomolecular Research, Faculty of Science, Department of Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
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  • Koen M. Visscher,

    1. Bijvoet Center for Biomolecular Research, Faculty of Science, Department of Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
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  • Aalt D. J. van Dijk,

    1. Applied Bioinformatics, Department of Bioscience, Wageningen UR, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
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  • Alexandre M. J. J. Bonvin

    Corresponding author
    1. Bijvoet Center for Biomolecular Research, Faculty of Science, Department of Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
    • Bijvoet Center for Biomolecular Research, Faculty of Science, Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
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Abstract

HADDOCK is one of the few docking programs that can explicitly account for water molecules in the docking process. Its solvated docking protocol starts from hydrated molecules and a fraction of the resulting interfacial waters is subsequently removed in a biased Monte Carlo procedure based on water-mediated contact probabilities. The latter were derived from an analysis of water contact frequencies from high-resolution crystal structures. Here, we introduce a simple water-mediated amino acid–amino acid contact probability scale derived from the Kyte-Doolittle hydrophobicity scale and assess its performance on the largest high-resolution dataset developed to date for solvated docking. Both scales yield high-quality docking results. The novel and simple hydrophobicity scale, which should reflect better the physicochemical principles underlying contact propensities, leads to a performance improvement of around 10% in ranking, cluster quality and water recovery at the interface compared with the statistics-based original solvated docking protocol. Proteins 2013. © 2012 Wiley Periodicals, Inc.

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