TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique
TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique
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TMSmesh：使用跟踪技术生成分子表面网格的稳健方法
DOI：
10.1021/ct100376g
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发表时间：
2011-01-01
影响因子：
5.5
通讯作者：
Lu, Benzhuo
中科院分区：
文献类型：
--
作者：
Chen, Minxin;Lu, Benzhuo
近期生物分子的现实数学建模和数值模拟的发展，尤其是隐式溶剂建模（例如，参见B. Z. Lu等人，Commun. Comput. Phys. 2008, 3, 973 - 1009中的综述）似乎需要合格、稳定且高效的分子表面网格划分。在本文中，我们提出了一种新方法：追踪分子表面进行网格划分（TMSmesh）生物分子的高斯面。该方法通过直接求解非线性方程计算表面点，通过追踪技术连接表面点进行多边形化，最后输出一个三角网格。TMSmesh相对于原子数量具有线性复杂度，并且能够处理由超过一百万个原子组成的分子，这对于分子可视化和几何分析中现有的表面生成方法通常是困难的。此外，由TMSmesh生成的网格在泊松 - 玻尔兹曼方程的边界元解中成功进行了测试，这直接为模拟大规模分子系统的静电溶剂化提供了一种途径。TMSmesh的二进制版本以及一组具有代表性的PQR基准分子可在我们的网页http://lsec.cc.ac.cn/∼lubz/Meshing.html下载。
Qualified, stable, and efficient molecular surface meshing appears to be necessitated by recent developments for realistic mathematical modeling and numerical simulation of biomolecules, especially in implicit solvent modeling (e.g., see a review in B. Z. Lu et al. Commun. Comput. Phys. 2008, 3, 973-1009). In this paper, we present a new method: tracing molecular surface for meshing (TMSmesh) the Gaussian surface of biomolecules. The method computes the surface points by solving a nonlinear equation directly, polygonizes by connecting surface points through a trace technique, and finally outputs a triangulated mesh. TMSmesh has a linear complexity with respect to the number of atoms and is shown to be capable of handling molecules consisting of more than one million atoms, which is usually difficult for the existing methods for surface generation used in molecular visualization and geometry analysis. Moreover, the meshes generated by TMSmesh are successfully tested in boundary element solutions of the Poisson-Boltzmann equation, which directly gives rise to a route to simulate electrostatic solvation of large-scale molecular systems. The binary version of TMSmesh and a set of representative PQR benchmark molecules are downloadable at our Web page http://lsec.cc.ac.cn/similar to lubz/Meshing.html.