PBEQ-Solver for online visualization of electrostatic potential of biomolecules.
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 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.
Jo
Sunhwan
S
Department of Chemistry, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA.
Vargyas
Miklos
M
Vasko-Szedlar
Judit
J
Roux
Benoît
B
Im
Wonpil
W
D002462:Cell Membrane / Q000737:chemistry; D003196:Computer Graphics; D004247:DNA / Q000737:chemistry; D030562:Databases, Protein; D020407:Internet; D008432:Mathematical Computing; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D012313:RNA / Q000737:chemistry; D012984:Software; D055672:Static Electricity
D011506:Proteins; D012313:RNA; D004247:DNA