Department of Mathematics, University of Michigan, Ann Arbor, Michigan, USA.
J Comput Chem. 2021 Aug 15;42(22):1552-1560. doi: 10.1002/jcc.26692. Epub 2021 May 26.
The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of solvated biomolecules. In this model the dielectric interface between the biomolecule and solvent is often taken to be the molecular surface or solvent-excluded surface (SES), and the quality of the SES triangulation is critical in boundary element simulations of the model. This work compares the performance of the MSMS and NanoShaper surface triangulation codes for a set of 38 biomolecules. While MSMS produces triangles of exceedingly small area and large aspect ratio, the two codes yield comparable values for the SES surface area and electrostatic solvation energy, where the latter calculations were performed using the treecode-accelerated boundary integral (TABI) PB solver. However we found that NanoShaper is computationally more efficient and reliable than MSMS, especially when parameters are set to produce highly resolved triangulations.
泊松-玻尔兹曼（PB）隐式溶剂模型是研究溶剂化生物分子静电的常用框架。在该模型中，生物分子和溶剂之间的介电界面通常取为分子表面或溶剂排斥表面（SES），SES 三角剖分的质量在模型的边界元模拟中至关重要。这项工作比较了 MSMS 和 NanoShaper 表面三角剖分代码在 38 个生物分子上的性能。虽然 MSMS 生成的三角形面积极小且纵横比很大，但这两个代码对于 SES 表面积和静电溶剂化能的值是可比的，后者的计算使用了树码加速边界积分（TABI）PB 求解器。然而，我们发现 NanoShaper 比 MSMS 更有效率和可靠，尤其是在设置参数以产生高分辨率三角剖分时。
