An Algebraic Spline Model of Molecular Surfaces for Energetic Computations

doi:10.1109/TCBB.2011.81

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	An Algebraic Spline Model of Molecular Surfaces for Energetic Computations
	Zhao, Wenqi 1; Xu, Guoliang 2; Bajaj, Chandrajit 3
	2011-11-01
发表期刊	IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
ISSN	1545-5963
卷号	8 期号:6 页码:1458-1467
摘要	In this paper, we describe a new method to generate a smooth algebraic spline (AS) approximation of the molecular surface (MS) based on an initial coarse triangulation derived from the atomic coordinate information of the biomolecule, resident in the Protein data bank (PDB). Our method first constructs a triangular prism scaffold covering the PDB structure, and then generates a piecewise polynomial F on the Bernstein-Bezier (BB) basis within the scaffold. An ASMS model of the molecular surface is extracted as the zero contours of F, which is nearly C(1) and has dual implicit and parametric representations. The dual representations allow us easily do the point sampling on the ASMS model and apply it to the accurate estimation of the integrals involved in the electrostatic solvation energy computations. Meanwhile comparing with the trivial piecewise linear surface model, fewer number of sampling points are needed for the ASMS, which effectively reduces the complexity of the energy estimation.
关键词	Polynomial splines molecular surfaces prismatic scaffolds Bernstein-Bezier basis solvation energetics error bounds rate of convergence
DOI	10.1109/TCBB.2011.81
语种	英语
资助项目	US National Science Foundation (NSF)[CNS-0540033] ; NIH[R01-EB00487] ; NIH[R01-GM074258] ; NIH[R01-GM07308] ; J.T. Oden ICES visitor fellowship
WOS研究方向	Biochemistry & Molecular Biology ; Computer Science ; Mathematics
WOS类目	Biochemical Research Methods ; Computer Science, Interdisciplinary Applications ; Mathematics, Interdisciplinary Applications ; Statistics & Probability
WOS记录号	WOS:000294782100002
出版者	IEEE COMPUTER SOC
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/12850
专题	中国科学院数学与系统科学研究院
通讯作者	Zhao, Wenqi
作者单位	1.Univ Texas Austin, Ctr Computat Visualizat, Inst Computat Engn & Sci, Austin, TX 78712 USA 2.Chinese Acad Sci, Inst Computat Math & Sci Engn Comp, Beijing, Peoples R China 3.Univ Texas Austin, Dept Comp Sci, Inst Computat Engn & Sci, Austin, TX 78712 USA
推荐引用方式 GB/T 7714	Zhao, Wenqi,Xu, Guoliang,Bajaj, Chandrajit. An Algebraic Spline Model of Molecular Surfaces for Energetic Computations[J]. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,2011,8(6):1458-1467.
APA	Zhao, Wenqi,Xu, Guoliang,&Bajaj, Chandrajit.(2011).An Algebraic Spline Model of Molecular Surfaces for Energetic Computations.IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,8(6),1458-1467.
MLA	Zhao, Wenqi,et al."An Algebraic Spline Model of Molecular Surfaces for Energetic Computations".IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 8.6(2011):1458-1467.