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Nucleic Acids Research Advance Access published online on May 8, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm276
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

Todd J. Dolinsky1, Paul Czodrowski2, Hui Li3, Jens E. Nielsen4, Jan H. Jensen5, Gerhard Klebe2 and Nathan A. Baker1,*

1Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St. Louis, 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110, USA, 2Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany, 3Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA, 4School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland and 5Department of Chemistry, University of Copenhagen, Copenhagen, Denmark

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

Received January 31, 2007. Revised April 7, 2007. Accepted April 11, 2007.

Real-world observable physical and chemical characteristics are increasingly being calculated from the 3D structures of biomolecules. Methods for calculating pKa values, binding constants of ligands, and changes in protein stability are readily available, but often the limiting step in computational biology is the conversion of PDB structures into formats ready for use with biomolecular simulation software. The continued sophistication and integration of biomolecular simulation methods for systems- and genome-wide studies requires a fast, robust, physically realistic and standardized protocol for preparing macromolecular structures for biophysical algorithms. As described previously, the PDB2PQR web server addresses this need for electrostatic field calculations (Dolinsky et al., Nucleic Acids Research, 32, W665–W667, 2004). Here we report the significantly expanded PDB2PQR that includes the following features: robust standalone command line support, improved pKa estimation via the PROPKA framework, ligand parameterization via PEOE_PB charge methodology, expanded set of force fields and easily incorporated user-defined parameters via XML input files, and improvement of atom addition and optimization code. These features are available through a new web interface (http://pdb2pqr.sourceforge.net/), which offers users a wide range of options for PDB file conversion, modification and parameterization.


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