caa a22 4500 60551318X CHVBK 20210128100659.0 cr unu---uuuuu 210128e20150501xx s 000 0 eng 10.1007/s00894-015-2654-9 doi (NATIONALLICENCE)springer-10.1007/s00894-015-2654-9 Parameterization for molecular Gaussian surface and a comparison study of surface mesh generation [Elektronische Daten] [Tiantian Liu, Minxin Chen, Benzhuo Lu] 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. Springer-Verlag Berlin Heidelberg, 2015 Molecular Gaussian surface nationallicence Parameterization nationallicence Mesh quality nationallicence Meshing software nationallicence Solvation energy nationallicence Liu Tiantian 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, 100190, Beijing, China aut Chen Minxin Center for System Biology, Department of Mathematics, Soochow University, 215006, Suzhou, China aut Lu Benzhuo 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, 100190, Beijing, China aut Journal of Molecular Modeling Springer Berlin Heidelberg 21/5(2015-05-01), 1-14 1610-2940 21:5<1 2015 21 894 https://doi.org/10.1007/s00894-015-2654-9 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00894-015-2654-9 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Liu Tiantian 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, 100190, Beijing, China aut NATIONALLICENCE 700 1- Chen Minxin Center for System Biology, Department of Mathematics, Soochow University, 215006, Suzhou, China aut NATIONALLICENCE 700 1- Lu Benzhuo 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, 100190, Beijing, China aut NATIONALLICENCE 773 0- Journal of Molecular Modeling Springer Berlin Heidelberg 21/5(2015-05-01), 1-14 1610-2940 21:5<1 2015 21 894