KMS Of Academy of mathematics and systems sciences, CAS
| An Algebraic Spline Model of Molecular Surfaces for Energetic Computations | |
| Zhao, Wenqi1; Xu, Guoliang2; Bajaj, Chandrajit3 | |
| 2011-11-01 | |
| Source Publication | IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
 |
| ISSN | 1545-5963 |
| Volume | 8Issue:6Pages:1458-1467 |
| Abstract | 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. |
| Keyword | Polynomial splines molecular surfaces prismatic scaffolds Bernstein-Bezier basis solvation energetics error bounds rate of convergence |
| DOI | 10.1109/TCBB.2011.81 |
| Language | 英语 |
| Funding Project | US National Science Foundation (NSF)[CNS-0540033] ; NIH[R01-EB00487] ; NIH[R01-GM074258] ; NIH[R01-GM07308] ; J.T. Oden ICES visitor fellowship |
| WOS Research Area | Biochemistry & Molecular Biology ; Computer Science ; Mathematics |
| WOS Subject | Biochemical Research Methods ; Computer Science, Interdisciplinary Applications ; Mathematics, Interdisciplinary Applications ; Statistics & Probability |
| WOS ID | WOS:000294782100002 |
| Publisher | IEEE COMPUTER SOC |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/12850 |
| Collection | 中国科学院数学与系统科学研究院 |
| Affiliation | 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 |
| 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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