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Nucleic Acids Research 2004 32(Web Server Issue):W665-W667; doi:10.1093/nar/gkh381
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations

Todd J. Dolinsky, Jens E. Nielsen1,3, J. Andrew McCammon1,2 and Nathan A. Baker*

Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St Louis, 700 S. Euclid Avenue, Campus Box 8036, St Louis, MO 63110, USA, 1 Department of Chemistry and Biochemistry and 2 Department of Pharmacology, Center for Theoretical Biological Physics, Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, Mail Code 0365, La Jolla, CA 92093-0365, USA and 3 Department of Biochemistry, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland

* To whom correspondence should be addressed. Tel: +1 314 362 2040; Fax: +1 314 362 0234; Email: baker{at}biochem.wustl.edu

Received February 10, 2004; Revised and Accepted March 15, 2004

Continuum solvation models, such as Poisson–Boltzmann and Generalized Born methods, have become increasingly popular tools for investigating the influence of electrostatics on biomolecular structure, energetics and dynamics. However, the use of such methods requires accurate and complete structural data as well as force field parameters such as atomic charges and radii. Unfortunately, the limiting step in continuum electrostatics calculations is often the addition of missing atomic coordinates to molecular structures from the Protein Data Bank and the assignment of parameters to biomolecular structures. To address this problem, we have developed the PDB2PQR web service (http://agave.wustl.edu/pdb2pqr/). This server automates many of the common tasks of preparing structures for continuum electrostatics calculations, including adding a limited number of missing heavy atoms to biomolecular structures, estimating titration states and protonating biomolecules in a manner consistent with favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields, and finally generating ‘PQR’ output compatible with several popular computational biology packages. This service is intended to facilitate the setup and execution of electrostatics calculations for both experts and non-experts and thereby broaden the accessibility to the biological community of continuum electrostatics analyses of biomolecular systems.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.


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