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Bioinformatics Advance Access originally published online on August 9, 2006
Bioinformatics 2006 22(19):2340-2347; doi:10.1093/bioinformatics/btl395
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Solvated docking: introducing water into the modelling of biomolecular complexes

Aalt D. J. van Dijk and Alexandre M. J. J. Bonvin *

Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University 3584CH, Utrecht, The Netherlands

*To whom correspondence should be addressed.

Motivation: Interfacial water, which plays an important role in mediating biomolecular interactions, has been neglected in the modelling of biomolecular complexes.

Methods: We present a solvated docking approach that explicitly accounts for the presence of water in protein–protein complexes. Our solvated docking protocol is based on the concept of the first encounter complex in which a water layer is present in-between the molecules. It mimics the pathway from this initial complex towards the final assembly in which most waters have been expelled from the interface. Docking is performed from solvated biomolecules and waters are removed in a biased Monte Carlo procedure based on water-mediated contact propensities obtained from an analysis of high-resolution crystal structures.

Results: We demonstrate the feasibility of this approach for protein–protein complexes representing both ‘wet’ and ‘dry’ interfaces. Solvated docking leads to improvements both in quality and scoring. Water molecules are recovered that closely match the ones in the crystal structures.

Availabilty: Solvated docking will be made available in the future release of HADDOCK version 2.0 (http://www.nmr.chem.uu.nl/haddock).

Contact: a.m.j.j.bonvin{at}chem.uu.nl

Supplementary information: Supplementary Data are available at Bioinformatics Online.

Received on May 10, 2005; revised on June 26, 2006; accepted on July 17, 2006

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