Parameterization for molecular Gaussian surface and a comparison study of surface mesh generation

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• 作者：Tiantian Liu (1)
  Minxin Chen (2)
  Benzhuo Lu (1)
  
  1. State Key Laboratory of Scientific and Engineering Computing ; National Center for Mathematics and Interdisciplinary Sciences ; Academy of Mathematics and Systems Science ; Chinese Academy of Sciences ; Beijing ; 100190 ; China
  2. Center for System Biology ; Department of Mathematics ; Soochow University ; Suzhou ; 215006 ; China
  
• 关键词：Molecular Gaussian surface ; Parameterization ; Mesh quality ; Meshing software ; Solvation energy
• 刊名：Journal of Molecular Modeling
• 出版年：2015
• 出版时间：May 2015
• 年：2015
• 卷：21
• 期：5
• 全文大小：2,362 KB
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• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Computer Applications in Chemistry
  Biomedicine
  Molecular Medicine
  Health Informatics and Administration
  Life Sciences
  Computer Application in Life Sciences
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：0948-5023

文摘

The molecular Gaussian surface has been frequently used in the field of molecular modeling and simulation. Typically, the Gaussian surface is defined using two controlling parameters; the decay rate and isovalue. Currently, there is a lack of studies in which a systematic approach in the determination of optimal parameterization according to the geometric features has been done. In this paper, surface area, volume enclosed by the surface and Hausdorff distance are used as three criteria for the parameterization to make the Gaussian surface approximate the solvent excluded surface (SES) well. For each of these three criteria, a search of the parameter space is carried out in order to determine the optimal parameter values. The resulted parameters are close to each other and result in similar calculated molecular properties. Approximation of the VDW surface is also done by analyzing the explicit expressions of the Gaussian surface and VDW surface, which analysis and parameters can be similarly applied to the solvent accessible surface (SAS) due to its geometric similarity to the VDW surface. Once the optimal parameters are obtained, we compare the performance of our Gaussian surface generation software TMSmesh with other commonly used software programs, focusing primarily on mesh quality and fidelity. Additionally, the Poisson-Boltzmann solvation energies based on the surface meshes generated by TMSmesh and those generated by other software programs are calculated and compared for a set of molecules with different sizes. The results of these comparisons validate both the accuracy and the applicability of the parameterized Gaussian surface.