Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces
Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces
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DOI：
10.1002/(sici)1096-987x(199903)20:4
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发表时间：
1999-03
影响因子：
3
通讯作者：
D. Ritchie;G. Kemp
中科院分区：
文献类型：
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作者：
D. Ritchie;G. Kemp
描述了一种快速生成大分子表面形状的近似参数表示的过程。该参数化用实球调和基函数的展开表示。使用参数表示的优点是可以通过使用拟牛顿算法来匹配一对曲面，以最小化适当选择的目标函数。当任务是在旋转搜索空间中进行搜索时，球谐函数是一种自然而方便的基函数选择。特别是，分子表面的旋转可以通过只旋转调和展开系数来模拟。这一旋转性质首次应用于三维分子相似性问题，其中一对相似的大分子表面将被最大限度地重叠。该方法是通过抗体重链可变区的叠加来实现的。对计算效率给予了特别关注。基于正二十面体的镶嵌，采用快速曲面采样和积分方法确定球谐展开系数。在当代工作站上，低分辨率曲面可以在10岁以下的S生成并显示，一对曲面可以在3岁以下的S最大限度地叠加显示。©1999 John Wiley&Sons，Inc.J Comput Chem 20：383-395,1999
A procedure that rapidly generates an approximate parametric representation of macromolecular surface shapes is described. The parametrization is expressed as an expansion of real spherical harmonic basis functions. The advantage of using a parametric representation is that a pair of surfaces can be matched by using a quasi‐Newton algorithm to minimize a suitably chosen objective function. Spherical harmonics are a natural and convenient choice of basis function when the task is one of search in a rotational search space. In particular, rotations of a molecular surface can be simulated by rotating only the harmonic expansion coefficients. This rotational property is applied for the first time to the 3‐dimensional molecular similarity problem in which a pair of similar macromolecular surfaces are to be maximally superposed. The method is demonstrated with the superposition of antibody heavy chain variable domains. Special attention is given to computational efficiency. The spherical harmonic expansion coefficients are determined using fast surface sampling and integration schemes based on the tessellation of a regular icosahedron. Low resolution surfaces can be generated and displayed in under 10 s and a pair of surfaces can be maximally superposed in under 3 s on a contemporary workstation. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 383–395, 1999