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An Algebraic Spline Model of Molecular Surfaces for Energetic Computations

机译:用于能量计算的分子表面的代数样条模型

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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.
机译:在本文中,我们描述了一种新方法,该方法基于驻留在蛋白质数据库(PDB)中的生物分子的原子坐标信息得出的初始粗三角剖分,来生成分子表面(MS)的光滑代数样条(AS)近似)。我们的方法首先构造一个覆盖PDB结构的三角棱镜支架,然后在支架中基于Bernstein-Bezier(BB)的基础生成分段多项式F。提取分子表面的ASMS模型作为F的零等高线,其近似C ^ 1,并具有隐式和参数双重表示。对偶表示使我们可以轻松地在ASMS模型上进行点采样,并将其应用于对静电溶剂化能量计算中涉及的积分的准确估计。同时,与平凡的分段线性曲面模型相比,ASMS所需的采样点数量更少,有效地降低了能量估算的复杂性。

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