SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson‐Boltzmann equation

• Published in: Journal of computational chemistry Vol. 38; no. 8; pp. 541 - 552
• Main Authors: Xie, Yang, Ying, Jinyong, Xie, Dexuan
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 30.03.2017
• Subjects: 3Dmol.js; Algorithms; biomolecular electrostatics; Electrostatics; Finite Element Analysis; finite element method; interactive visualization; Particle Size; Poisson Distribution; Proteins - chemistry; size modified Poisson‐Boltzmann equation; Static Electricity; Thermodynamics; User interface; User-Computer Interface; Web Browser; size modified Poisson-Boltzmann equation; biomolecular electrostatics; finite element method; interactive visualization; 3Dmol.js
• ISSN: 0192-8651; 1096-987X; 1096-987X
• DOI: 10.1002/jcc.24703

SMPBS (Size Modified Poisson‐Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson‐Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson‐Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile‐friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware‐accelerated molecular visualization viewer based on the 3Dmol.js library. In particular, the viewer allows computed electrostatics to be directly mapped onto an irregular triangular mesh of a molecular surface. Due to this functionality and the fast SMPBE finite element solvers, the web server is very efficient in the calculation and visualization of electrostatics. In addition, SMPBE is reconstructed using a new objective electrostatic free energy, clearly showing that the electrostatics and ionic concentrations predicted by SMPBE are optimal in the sense of minimizing the objective electrostatic free energy. SMPBS is available at the URL: smpbs.math.uwm.edu © 2017 Wiley Periodicals, Inc. SMPBS (smpbs.math.uwm.edu) is a web server for computing and visualizing biomolecular electrostatics using finite element solvers of the size modified Poisson‐Boltzmann equation (SMPBE). It features an interactive, hardware‐accelerated molecular visualization viewer, based on the 3Dmol.js library, that allows computed electrostatics to be directly mapped onto an irregular triangular mesh of a molecular surface. It also enables efficient calculation of electrostatic solvation and binding free energies. Furthermore, SMPBE is shown to be optimal in the sense of minimizing a new objective electrostatic free energy subject to an ionic size constraint, and can be a more versatile substitute for classic PBE.