Name
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) proteinprotein (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 angstrom before and 1 angstrom 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. |
Year | DOI | Venue |
|---|---|---|
2008 | 10.1093/nar/gkn314 | NUCLEIC ACIDS RESEARCH |
Keywords | Field | DocType |
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.,electrostatic potential,rna,dna,poisson boltzmann,graphic user interface,interactive visualization,finite difference,computer graphics,java applet,static electricity,free energy,proteins,internet | Electrostatics,Biology,Visualization,Graphical user interface,Software,Computational science,Solvation,Solver,Java applet,Genetics,Software visualization | Journal |
Volume | Issue | ISSN |
36 | Web Server issue | 0305-1048 |
Citations | PageRank | References |
11 | 0.84 | 14 |
Authors | ||
5 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Sunhwan Jo | 1 | 134 | 13.08 |
| Miklos Vargyas | 2 | 13 | 1.21 |
| Judit Vasko-Szedlar | 3 | 11 | 0.84 |
| Benoît Roux | 4 | 11 | 0.84 |
| Wonpil Im | 5 | 163 | 17.39 |