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SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson‐Boltzmann equation
Author(s) -
Xie Yang,
Ying Jinyong,
Xie Dexuan
Publication year - 2017
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.24703
Subject(s) - poisson–boltzmann equation , computer science , computational science , electrostatics , finite element method , poisson's equation , poisson distribution , boltzmann equation , statistical physics , mathematics , physics , mathematical analysis , quantum mechanics , thermodynamics , ion , statistics
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.