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An Algebraic Spline Model of Molecular Surfaces for Energetic Computations
Zhao, Wenqi1; Xu, Guoliang2; Bajaj, Chandrajit3
2011-11-01
Source PublicationIEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
ISSN1545-5963
Volume8Issue:6Pages:1458-1467
AbstractIn 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.
KeywordPolynomial splines molecular surfaces prismatic scaffolds Bernstein-Bezier basis solvation energetics error bounds rate of convergence
DOI10.1109/TCBB.2011.81
Language英语
Funding ProjectUS National Science Foundation (NSF)[CNS-0540033] ; NIH[R01-EB00487] ; NIH[R01-GM074258] ; NIH[R01-GM07308] ; J.T. Oden ICES visitor fellowship
WOS Research AreaBiochemistry & Molecular Biology ; Computer Science ; Mathematics
WOS SubjectBiochemical Research Methods ; Computer Science, Interdisciplinary Applications ; Mathematics, Interdisciplinary Applications ; Statistics & Probability
WOS IDWOS:000294782100002
PublisherIEEE COMPUTER SOC
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Cited Times:1[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/12850
Collection中国科学院数学与系统科学研究院
Affiliation1.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
Recommended Citation
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.
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