title: SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson-Boltzmann equation.
abstract: 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.
authors.affiliation: Department of Computer Science, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, 53201.
authors.forename: Yang
authors.initials: Y
authors.lastname: Xie
authors.affiliation: Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, 53201.
authors.forename: Jinyong
authors.initials: J
authors.lastname: Ying
authors.affiliation: Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, 53201.
authors.forename: Dexuan
authors.initials: D
authors.lastname: Xie
mesh_terms: D000465:Algorithms; D020342:Finite Element Analysis; D010316:Particle Size; D016012:Poisson Distribution; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity; D013816:Thermodynamics; D014584:User-Computer Interface; D064878:Web Browser
chemical_list: D011506:Proteins
keywords: 3Dmol.js; biomolecular electrostatics; finite element method; interactive visualization; size modified Poisson-Boltzmann equation