论文标题
Tabi Poisson-Boltzmann求解器中的MSM和纳米蛋白分子表面三角测量代码的比较
Comparison of the MSMS and NanoShaper molecular surface triangulation codes in the TABI Poisson--Boltzmann solver
论文作者
论文摘要
Poisson-Boltzmann（PB）隐式溶剂模型是研究浸入水中的生物分子的静电框架。在此模型中，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除的表面（SES），而SES三角测量的质量在PB模型的边界元素模拟中至关重要。在这项工作中，我们比较了一组38个生物分子的MSM和纳米蛋白表面三角测量代码。尽管MSMS产生了极小面积和较大纵横比的三角形，但两个代码产生了SES表面积和静电溶剂化能的可比值，其中使用TreeCode-Accelerated边界积分（TABI）PB求解器进行了后一个计算。但是，我们发现，纳米蛋白比MSM更有效，更可靠，尤其是当参数设置为产生高度分辨的三角剖分时。
The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of biomolecules immersed in water with dissolved salt. 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 PB model. In this work we compare 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 more efficient and reliable than MSMS, especially when parameters are set to produce highly resolved triangulations.
