Quality meshing of implicit solvation models of biomolecular structures

doi:10.1016/j.cagd.2006.01.008

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	Quality meshing of implicit solvation models of biomolecular structures
	Zhang, Yongjie ; Xu, Guoliang ; Bajaj, Chandrajit
	2006-08-01
发表期刊	COMPUTER AIDED GEOMETRIC DESIGN
ISSN	0167-8396
卷号	23 期号:6 页码:510-530
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.
关键词	quality mesh biomolecule implicit solvation model finite element simulation
DOI	10.1016/j.cagd.2006.01.008
语种	英语
WOS研究方向	Computer Science ; Mathematics
WOS类目	Computer Science, Software Engineering ; Mathematics, Applied
WOS记录号	WOS:000239260900004
出版者	ELSEVIER SCIENCE BV
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/3408
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.