PBEQ-Solver

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.


References in zbMATH (referenced in 12 articles )

Showing results 1 to 12 of 12.
Sorted by year (citations)

  1. Chen, Duan: A new Poisson-Nernst-Planck model with ion-water interactions for charge transport in ion channels (2016)
  2. Xie, Dexuan; Ying, Jinyong: A new box iterative method for a class of nonlinear interface problems with application in solving Poisson-Boltzmann equation (2016)
  3. Cang, Zixuan; Mu, Lin; Wu, Kedi; Opron, Kristopher; Xia, Kelin; Wei, Guo-Wei: A topological approach for protein classification (2015)
  4. Jiang, Yi; Xie, Yang; Ying, Jinyong; Xie, Dexuan; Yu, Zeyun: SDPBS web server for calculation of electrostatics of ionic solvated biomolecules (2015)
  5. Ying, Jinyong; Xie, Dexuan: A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule (2015)
  6. Chen, Duan: Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules (2014)
  7. Chen, Duan: Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules (2014)
  8. Jiang, Yi; Ying, Jinyong; Xie, Dexuan: A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications (2014)
  9. Xie, Dexuan: New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics (2014)
  10. Xie, Dexuan; Jiang, Yi; Ying, Jinyong: A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications (2014)
  11. Xie, Dexuan; Scott, L. Ridgway: A new boundary integral equation for molecular electrostatics with charges over whole space (2011)
  12. Jo, Sunhwan; Vargyas, Miklós; Vasko-Szedlar, Judit; Roux, Benoît; Im, Wonpil: PBEQ-solver for online visualization of electrostatic potential of biomolecules (2008) ioport