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Quality meshing of implicit solvation models of biomolecular structures

文献类型：期刊论文

作者Zhang, Yongjie; Xu, Guoliang; Bajaj, Chandrajit
刊名COMPUTER AIDED GEOMETRIC DESIGN
出版日期2006-08-01
卷号23期号:6页码:510-530
关键词quality mesh biomolecule implicit solvation model finite element simulation
ISSN号0167-8396
DOI10.1016/j.cagd.2006.01.008
英文摘要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.
WOS研究方向Computer Science ; Mathematics
语种英语
WOS记录号WOS:000239260900004
出版者ELSEVIER SCIENCE BV
源URL[http://ir.amss.ac.cn/handle/2S8OKBNM/3407]  
专题中国科学院数学与系统科学研究院
通讯作者Bajaj, Chandrajit
作者单位1.Univ Texas, Dept Comp Sci, Inst Computat Engn & Sci, Computat Visualizat Ctr, Austin, TX 78712 USA
2.Chinese Acad Sci, Acad Math & Syst Sci, Inst Computat Math, State Key Lab Sci & Engn Comp, Beijing 100080, Peoples R China
推荐引用方式
GB/T 7714		 Zhang, Yongjie,Xu, Guoliang,Bajaj, Chandrajit. Quality meshing of implicit solvation models of biomolecular structures[J]. COMPUTER AIDED GEOMETRIC DESIGN,2006,23(6):510-530.
APA Zhang, Yongjie,Xu, Guoliang,&Bajaj, Chandrajit.(2006).Quality meshing of implicit solvation models of biomolecular structures.COMPUTER AIDED GEOMETRIC DESIGN,23(6),510-530.
MLA Zhang, Yongjie,et al."Quality meshing of implicit solvation models of biomolecular structures".COMPUTER AIDED GEOMETRIC DESIGN 23.6(2006):510-530.

入库方式： OAI收割

来源：数学与系统科学研究院

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