期刊
COMPUTER AIDED GEOMETRIC DESIGN
卷 23, 期 6, 页码 510-530出版社
ELSEVIER
DOI: 10.1016/j.cagd.2006.01.008
关键词
quality mesh; biomolecule; implicit solvation model; finite element simulation
资金
- NCRR NIH HHS [P41 RR002250-200095, P41 RR008605, P41 RR002250, P41 RR002250-217415, P41 RR008605-158485, P41 RR008605-147784, P41 RR002250-226519, P20 RR020647, P41 RR008605-147779, P41 RR008605-158490] Funding Source: Medline
- NIGMS NIH HHS [R01 GM073087-01A1, R01 GM074258, R01 GM074258-01, R01 GM073087, R01 GM074258-02] Funding Source: Medline
This paper describes a comprehensive approach to construct quality meshes for implicit solvation models of biomolecular structures starting from atomic resolution data in the Protein Data Bank (PDB). First, a smooth volumetric electron density map is constructed from atomic data using weighted Gaussian isotropic kernel functions and a two-level clustering technique. This enables the selection of a smooth implicit solvation surface approximation to the Lee-Richards molecular surface. Next, a modified dual contouring method is used to extract triangular meshes for the surface, and tetrahedral meshes for the volume inside or outside the molecule within a bounding sphere/box of influence. Finally, geometric flow techniques are used to improve the surface and volume mesh quality. Several examples are presented, including generated meshes for biomolecules that have been successfully used in finite element simulations involving solvation energetics and binding rate constants. (C) 2006 Elsevier B.V. All rights reserved.
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