Gui Sheng, Khan Dawar, Wang Qin, Yan Dong-Ming, Lu Ben-Zhuo
LSEC, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Vis Comput Ind Biomed Art. 2018 Sep 5;1(1):7. doi: 10.1186/s42492-018-0007-0.
With the development of biomolecular modeling and simulation, especially implicit solvent modeling, higher requirements are set for the stability, efficiency and mesh quality of molecular mesh generation software. In this review, we summarize the recent works in biomolecular mesh generation and molecular visualization. First, we introduce various definitions of molecular surface and corresponding meshing software. Second, as the mesh quality significantly influences biomolecular simulation, we investigate some remeshing methods in the fields of computer graphics and molecular modeling. Then, we show the application of biomolecular mesh in the boundary element method (BEM) and the finite element method (FEM). Finally, to conveniently visualize the numerical results based on the mesh, we present two types of molecular visualization systems.
随着生物分子建模与模拟技术的发展，尤其是隐式溶剂建模技术的发展，对分子网格生成软件的稳定性、效率和网格质量提出了更高的要求。在这篇综述中，我们总结了生物分子网格生成和分子可视化方面的最新研究成果。首先，我们介绍了分子表面的各种定义以及相应的网格划分软件。其次，由于网格质量对生物分子模拟有显著影响，我们研究了计算机图形学和分子建模领域的一些重新网格化方法。然后，我们展示了生物分子网格在边界元法（BEM）和有限元法（FEM）中的应用。最后，为了方便地可视化基于网格的数值结果，我们介绍了两种类型的分子可视化系统。
