W270–W275 Nucleic Acids Research, 2008, Vol. 36, Web Server issue Published online 28 May 2008 doi:10.1093/nar/gkn314 PBEQ-Solver for online visualization of electrostatic potential of biomolecules Sunhwan Jo 1 , Miklos Vargyas 2 , Judit Vasko-Szedlar 2 , Benoıˆt Roux 3 and Wonpil Im 4, * 1 Department of Chemistry, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA, 2 ChemAxon Kft., Ma ´ ramaros ko ¨ z 3/a, Budapest, 1037 Hungary, 3 Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Sciences, W323B 929 East 57th Street, Chicago, IL 60637 and 4 Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA Received January 6, 2008; Revised April 25, 2008; Accepted May 7, 2008 ABSTRACT 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 mem- brane 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 inter- actively 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 Marvin- Space 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 A ˚ before and 1 A ˚ 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. INTRODUCTION Implicit solvent treatments are approximate methods that attempt to incorporate the average influence of the molecular environment on a system of interest without having to explicitly simulate the molecules constituting this environment (1). Implicit solvent methods have emerged as a popular strategy to approximate bulk solvent or membrane environments and have been applied successfully to protein–protein or protein–ligand binding thermodynamics, scoring of protein conformations in structure prediction, peptide and protein folding/unfold- ing studies and ion channels (1–4). In particular, Poisson- Boltzmann (PB) continuum electrostatics, in which the solvent is represented as a featureless dielectric material, is the most rigorous and popular method to estimate the electrostatic solvation energy of a solute with an arbitrary shape, and particular successes in applications to complex biological problems are evident (2,5–7). The characteriza- tion of the electrostatic potential on the macromolecular surface by solving the PB equation is becoming a routine practice in structural biology (5). Over the last two decades, considerable efforts have been made to generalize and enhance the computational methodologies and techniques to solve the PB equation and visualize the calculated electrostatic potential (7–13). As a result, various user-friendly programs that provide numerical solutions of the PB equation using finite- difference or finite-element methods with a discretized grid are now available as standalone software such as APBS (7), MEAD (14), Qnifft (15), DelPhi (16) and Zap (17), or as modules in biomolecular modeling and simulation programs such as PB solver (18) in AMBER (19), PBEQ (12,20–22) in CHARMM (23), APBS (7) in AMBER (7), CHARMM (23), TINKER (24) and NAMD (25), and PB solver (26) in Jaguar (http:// www.schrodinger.com). PyMOL (27), VMD (28), GRASP (29), PMV (30) and DINO (http://www.dino3d.org) (31) provide various visualization tools for calculated electro- static potentials. There are also several useful web-based interfaces to setup and perform PB calculations such as PDB2PQR (32), PCE (33) and PDB_Hydro (34). We have developed PBEQ-Solver (http://www.charmm- gui.org/input/pbeqsolver) to provide a web-based graphi- cal user interface (GUI) to read biomolecular protein data *To whom correspondence should be addressed. Tel: (785) 864 1993; Fax: (785) 864 5558; Email: wonpil@ku.edu ß 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. by on April 17, 2010 http://nar.oxfordjournals.org Downloaded from