Comparison of the MSMS and NanoShaper molecular surface triangulation codes in the TABI Poisson–Boltzmann solver
Comparison of the MSMS and NanoShaper molecular surface triangulation codes in the TABI Poisson–Boltzmann solver
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DOI：
10.1002/jcc.26692
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发表时间：
2020-10
影响因子：
3
通讯作者：
Leighton Wilson;R. Krasny
中科院分区：
文献类型：
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作者：
Leighton Wilson;R. Krasny
Poisson-Boltzmann（PB）隐式溶剂模型是研究溶剂化生物分子静电性质的一个常用框架。在该模型中，生物分子和溶剂之间的介电界面通常被视为分子表面或溶剂排斥表面（SES），SES三角测量的质量在模型的边界元模拟中至关重要。这项工作比较了一组38个生物分子的MSMS和NanoShaper表面三角测量代码的性能。虽然MSMS产生面积极小且长宽比较大的三角形，但两个代码产生的SES表面积和静电溶剂化能值相当，其中后者的计算是使用树码加速边界积分（TABI）PB求解器进行的。然而，我们发现NanoShaper在计算上比MSMS更有效和可靠，特别是当参数设置为产生高分辨率三角剖分时。
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.