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Nucleic Acids Research Advance Access published online on May 28, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn314
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© 2008 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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PBEQ-Solver for online visualization of electrostatic potential of biomolecules

Sunhwan Jo1, Miklos Vargyas2, Judit Vasko-Szedlar2, Benoît Roux3 and Wonpil Im4,*

1Department of Chemistry, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA, 2ChemAxon Kft., Máramaros köz 3/a, Budapest, 1037 Hungary, 3Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Sciences, W323B 929 East 57th Street, Chicago, IL 60637 and 4Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA

*To whom correspondence should be addressed. Tel: (785) 864 1993; Fax: (785) 864 5558; Email: wonpil{at}ku.edu

Received January 6, 2008. Revised April 25, 2008. Accepted May 7, 2008.

PBEQ-Solver provides a web-based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann (PB) equations and interactively visualize the electrostatic potential. PBEQ-Solver calculates (i) electrostatic potential and solvation free energy, (ii) protein–protein (DNA or RNA) electrostatic interaction energy and (iii) pKa of a selected titratable residue. All the calculations can be performed in both aqueous solvent and membrane environments (with a cylindrical pore in the case of membrane). PBEQ-Solver uses the PBEQ module in the biomolecular simulation program CHARMM to solve the finite-difference PB equation of molecules specified by users. Users can interactively inspect the calculated electrostatic potential on the solvent-accessible surface as well as iso-electrostatic potential contours using a novel online visualization tool based on MarvinSpace molecular visualization software, a Java applet integrated within CHARMM-GUI (http://www.charmm-gui.org). To reduce the computational time on the server, and to increase the efficiency in visualization, all the PB calculations are performed with coarse grid spacing (1.5 Å before and 1 Å after focusing). PBEQ-Solver suggests various physical parameters for PB calculations and users can modify them if necessary. PBEQ-Solver is available at http://www.charmm-gui.org/input/pbeqsolver.


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