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 Cited in: 14 Documents all top 5 Cited by 23 Authors 8 Xie, Dexuan 6 Ying, Jinyong 3 Chen, Duan 3 Jiang, Yi 1 Bochkov, Daniil 1 Cang, Zixuan 1 Chowdhury, Rochishnu 1 Debuhr, Jackson 1 Egan, Raphael 1 Gibou, Frédéric 1 Lu, Benzhuo 1 Mayolo, Silvio 1 Mu, Lin 1 Niedzielski, Drake 1 Opron, Kristopher 1 Scott, Larkin Ridgway 1 Sterling, Thomas Lawrence 1 Wei, Guowei 1 Wu, Kedi 1 Xia, Kelin 1 Xie, Yang 1 Yu, Zeyun 1 Zhang, Bo all top 5 Cited in 8 Serials 4 Molecular Based Mathematical Biology 3 Journal of Computational Physics 2 Computational and Mathematical Biophysics 1 Bulletin of Mathematical Biology 1 BIT 1 Journal of Computational and Applied Mathematics 1 Applied Mathematical Modelling 1 Communications in Computational Physics Cited in 5 Fields 10 Biology and other natural sciences (92-XX) 9 Numerical analysis (65-XX) 4 Optics, electromagnetic theory (78-XX) 3 Partial differential equations (35-XX) 2 Computer science (68-XX) Citations by Year