Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstr. 30, Bayreuth, Germany.
J Mol Model. 2010 Mar;16(3):419-29. doi: 10.1007/s00894-009-0541-y. Epub 2009 Jul 22.
In this paper, we describe a Monte Carlo method for determining the volume of a molecule. A molecule is considered to consist of hard, overlapping spheres. The surface of the molecule is defined by rolling a probe sphere over the surface of the spheres. To determine the volume of the molecule, random points are placed in a three-dimensional box, which encloses the whole molecule. The volume of the molecule in relation to the volume of the box is estimated by calculating the ratio of the random points placed inside the molecule and the total number of random points that were placed. For computational efficiency, we use a grid-cell based neighbor list to determine whether a random point is placed inside the molecule or not. This method in combination with a graph-theoretical algorithm is used to detect internal cavities and surface clefts of molecules. Since cavities and clefts are potential water binding sites, we place water molecules in the cavities. The potential water positions can be used in molecular dynamics calculations as well as in other molecular calculations. We apply this method to several proteins and demonstrate the usefulness of the program. The described methods are all implemented in the program McVol, which is available free of charge from our website at http://www.bisb.uni-bayreuth.de/software.html .
本文描述了一种用于确定分子体积的蒙特卡罗方法。分子被认为由硬重叠的球体组成。通过在球体表面滚动探针球来定义分子的表面。为了确定分子的体积，将随机点放置在一个三维盒子中，该盒子包围整个分子。通过计算放置在分子内部的随机点与放置的总随机点数的比例来估计分子的体积与盒子的体积之比。为了提高计算效率，我们使用基于网格单元的邻居列表来确定随机点是否放置在分子内部。这种方法与图论算法结合使用，用于检测分子的内部空腔和表面裂缝。由于空腔和裂缝是潜在的水结合位点，我们将水分子放置在空腔中。潜在的水分子位置可用于分子动力学计算以及其他分子计算。我们将此方法应用于几种蛋白质，并证明了该程序的有用性。描述的方法都在程序 McVol 中实现，该程序可从我们的网站免费获得，网址为 http://www.bisb.uni-bayreuth.de/software.html 。
