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

P. Kastritis, K.M. Visscher, A.D.J. van Dijk, A.M.J.J. Bonvin

Research output: Contribution to journalArticleAcademicpeer-review

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.
Original languageEnglish
Pages (from-to)510-518
Number of pages9
JournalProteins: Structure function and bioinformatics
Volume81
Issue number3
DOIs
Publication statusPublished - 2013

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