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Nucleic Acids Research 2006 34(Web Server issue):W38-W42; doi:10.1093/nar/gkl072
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© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson–Boltzmann treatment of macromolecule electrostatics

Cyril Azuara1, Erik Lindahl1,2, Patrice Koehl3, Henri Orland4 and Marc Delarue1,*

1 Unité de Dynamique Structurale des Macromolécules, URA 2185 du C.N.R.S., Institut Pasteur 75015 Paris, France 2 Computational Structural Biology, Stockholm Bioinformatics Center Stockholm, Sweden 3 Computer Science Department and Genome Center, University of California Davis, CA 95616, USA 4 Service de Physique Théorique, CE-Saclay 91191 Gif/Yvette Cedex, France

*To whom correspondence should be addressed at Unité de Dynamique Structurale des Macromolécules, URA 2185 du C.N.R.S., Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France. Tel: 33 1 45 68 86 05; Fax: 33 1 45 68 86 04; Email: delarue{at}pasteur.fr

Received February 14, 2006. Revised March 3, 2006. Accepted March 3, 2006.

We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized Poisson–Boltzmann–Langevin equation (GPBLE). We have implemented a web server (http://lorentz.immstr.pasteur.fr/pdb_hydro.php) that both numerically solves this equation and uses the resulting water density profiles to place water molecules at preferred sites of hydration. Surface atoms with high or low hydration preference can be easily displayed using a simple PyMol script, allowing for the tentative prediction of the dimerization interface in homodimeric proteins, or lipid binding regions in membrane proteins. The web site includes options that permit mutations in the sequence as well as reconstruction of missing side chain and/or main chain atoms. These tools are accessible independently from the electrostatics calculation, and can be used for other modeling purposes. We expect this web server to be useful to structural biologists, as the knowledge of solvent density should prove useful to get better fits at low resolution for X-ray diffraction data and to computational biologists, for whom these profiles could improve the calculation of interaction energies in water between ligands and receptors in docking simulations.


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