Vorobjev Y N, Hermans J
Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill 27599-7260, USA.
Biophys J. 1997 Aug;73(2):722-32. doi: 10.1016/S0006-3495(97)78105-0.
SIMS, a new method of calculating a smooth invariant molecular dot surface, is presented. The SIMS method generates the smooth molecular surface by rolling two probe spheres. A solvent probe sphere is rolled over the molecule and produces a Richards-Connolly molecular surface (MS), which envelops the solvent-excluded volume of the molecule. In deep crevices, Connolly's method of calculating the MS has two deficiencies. First, it produces self-intersecting parts of the molecular surface, which must be removed to obtain the correct MS. Second, the correct MS is not smooth, i.e., the direction of the normal vector of the MS is not continuous, and some points of the MS are singular. We present an exact method for removing self-intersecting parts and smoothing the singular regions of the MS. The singular MS is smoothed by rolling a smoothing probe sphere over the inward side of the singular MS. The MS in the vicinity of singularities is replaced with the reentrant surface of the smoothing probe sphere. The smoothing method does not disturb the topology of a singular MS, and the smooth MS is a better approximation of the dielectric border between high dielectric solvent and the low dielectric molecular interior. The SIMS method generates a smooth molecular dot surface, which has a quasi-uniform dot distribution in two orthogonal directions on the molecular surface, which is invariant with molecular rotation and stable under changes in the molecular conformation, and which can be used in a variety of implicit methods of modeling solvent effects. The SIMS program is faster than the Connolly MS program, and in a matter of seconds generates a smooth dot MS of a 200-residue protein. The program is available from the authors on request (see http:@femto.med.unc.edu/SIMS).
本文介绍了一种计算光滑不变分子点表面的新方法——SIMS。SIMS方法通过滚动两个探针球生成光滑的分子表面。一个溶剂探针球在分子上滚动，产生理查兹 - 康诺利分子表面（MS），该表面包围分子的溶剂排除体积。在深裂缝中，康诺利计算MS的方法存在两个缺陷。首先，它会产生分子表面的自相交部分，必须去除这些部分才能获得正确的MS。其次，正确的MS不光滑，即MS的法向量方向不连续，并且MS的一些点是奇异的。我们提出了一种精确的方法来去除自相交部分并平滑MS的奇异区域。通过在奇异MS的内侧滚动一个平滑探针球来平滑奇异的MS。奇异点附近的MS被平滑探针球的凹入表面所取代。平滑方法不会干扰奇异MS的拓扑结构，并且光滑的MS是高介电常数溶剂与低介电常数分子内部之间介电边界的更好近似。SIMS方法生成一个光滑的分子点表面，该表面在分子表面的两个正交方向上具有近似均匀的点分布，它随分子旋转而不变，并且在分子构象变化时稳定，可用于各种模拟溶剂效应的隐式方法。SIMS程序比康诺利MS程序更快，在几秒钟内就能生成一个200个残基蛋白质的光滑点MS。该程序可根据作者要求提供（见http:@femto.med.unc.edu/SIMS）。
