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PBEQ-Solver

swMATH ID: 17203
Software Authors: S. Jo, M. Vargyas, J. Vasko-Szedlar, B. Roux, W. Im
Description: 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 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.
Homepage: http://www.charmm-gui.org/?doc=input/pbeqsolver
Related Software: APBS; MIBPB; CHARMM; PDB2PQR; tabipb; TABI; DOLFIN; PETSc; DelPhi Web Server; FEniCS; IIMPACK; UHBD; SDPBS; GAMER; F2PY; DelPhi; SG; VCMM; DAFMPB; DASHMM
Referenced in: 14 Publications

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