SDPBS
SDPBS web server for calculation of electrostatics of ionic solvated biomolecules. The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. We recently developed a PBE solver library, called SDPBS, that incorporates the finite element, finite difference, solution decomposition, domain decomposition, and multigrid methods. To make SDPBS more accessible to the scientific community, we present an SDPBS web server in this paper that allows clients to visualize and manipulate the molecular structure of a biomolecule, and to calculate PBE solutions in a remote and user friendly fashion. The web server is available on the website url{https://lsextrnprod.uwm.edu/electrostatics/}.
Keywords for this software
References in zbMATH (referenced in 7 articles , 1 standard article )
Showing results 1 to 7 of 7.
Sorted by year (- Li, Jiao; Ying, Jinyong; Lu, Benzhuo: A flux-jump preserved gradient recovery technique for accurately predicting the electrostatic field of an immersed biomolecule (2019)
- Quan, Chaoyu; Stamm, Benjamin; Maday, Yvon: A domain decomposition method for the Poisson-Boltzmann solvation models (2019)
- Deng, Weishan; Xu, Jin; Zhao, Shan: On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics (2018)
- Ying, Jinyong; Xie, Dexuan: A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference (2018)
- Xie, Dexuan: New finite element iterative methods for solving a nonuniform ionic size modified Poisson-Boltzmann equation (2017)
- Xie, Dexuan; Jiang, Yi: A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules (2016)
- Jiang, Yi; Xie, Yang; Ying, Jinyong; Xie, Dexuan; Yu, Zeyun: SDPBS web server for calculation of electrostatics of ionic solvated biomolecules (2015)