SMPBS: Web Server for Computing Biomolecular Electrostatics Using Finite Element Solvers of Size Modified Poisson-Boltzmann Equation

作者：Xie Yang; Ying Jinyong; Xie Dexuan

来源：Journal of Computational Chemistry, 2017, 38(8): 541-552.

DOI：10.1002/jcc.24703

• size modified Poisson-Boltzmann equation-interactive visualization
• finite element method
• biomolecular electrostatics
• 3Dmol.js

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.

• 出版日期2017-3