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 language | English |
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Pages (from-to) | 510-518 |
Number of pages | 9 |
Journal | Proteins: Structure function and bioinformatics |
Volume | 81 |
Issue number | 3 |
DOIs | |
Publication status | Published - 2013 |