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 14 articles )

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  1. Zhang, Bo; Debuhr, Jackson; Niedzielski, Drake; Mayolo, Silvio; Lu, Benzhuo; Sterling, Thomas: DASHMM accelerated adaptive fast multipole Poisson-Boltzmann solver on distributed memory architecture (2019)
  2. Ying, Jinyong; Xie, Dexuan: A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference (2018)
  3. Chen, Duan: A new Poisson-Nernst-Planck model with ion-water interactions for charge transport in ion channels (2016)
  4. Xie, Dexuan; Ying, Jinyong: A new box iterative method for a class of nonlinear interface problems with application in solving Poisson-Boltzmann equation (2016)
  5. Cang, Zixuan; Mu, Lin; Wu, Kedi; Opron, Kristopher; Xia, Kelin; Wei, Guo-Wei: A topological approach for protein classification (2015)
  6. Jiang, Yi; Xie, Yang; Ying, Jinyong; Xie, Dexuan; Yu, Zeyun: SDPBS web server for calculation of electrostatics of ionic solvated biomolecules (2015)
  7. Ying, Jinyong; Xie, Dexuan: A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule (2015)
  8. Chen, Duan: Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules (2014)
  9. Chen, Duan: Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules (2014)
  10. Jiang, Yi; Ying, Jinyong; Xie, Dexuan: A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications (2014)
  11. Xie, Dexuan: New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics (2014)
  12. Xie, Dexuan; Jiang, Yi; Ying, Jinyong: A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications (2014)
  13. Xie, Dexuan; Scott, L. Ridgway: A new boundary integral equation for molecular electrostatics with charges over whole space (2011)
  14. Jo, Sunhwan; Vargyas, Miklós; Vasko-Szedlar, Judit; Roux, Benoît; Im, Wonpil: PBEQ-solver for online visualization of electrostatic potential of biomolecules (2008) ioport