THE DOUBLE CUBIC LATTICE METHOD - EFFICIENT APPROACHES TO NUMERICAL-INTEGRATION OF SURFACE-AREA AND VOLUME AND TO DOT SURFACE CONTOURING OF MOLECULAR ASSEMBLIES
THE DOUBLE CUBIC LATTICE METHOD - EFFICIENT APPROACHES TO NUMERICAL-INTEGRATION OF SURFACE-AREA AND VOLUME AND TO DOT SURFACE CONTOURING OF MOLECULAR ASSEMBLIES
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DOI：
10.1002/jcc.540160303
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发表时间：
1995-03-01
影响因子：
3
通讯作者：
SCHARF, M
中科院分区：
文献类型：
--
作者：
EISENHABER, F;LIJNZAAD, P;SCHARF, M
双立方晶格法 (DCLM) 是一种准确、快速的方法，用于计算分子表面积（例如溶剂可及表面或范德华表面）以及分子组装体的体积和致密性以及生成点表面。该算法没有特殊的内存要求，易于实现。计算速度极高，使得在单处理器工作站上可以对1000个及更多原子的系统进行曲面、体积和点曲面的交互式计算。该算法可以轻松并行化。 DCLM 是 Shrake 和 Rupley 提出的方法的算法变体（J. Mol. Biol., 79, 351-371, 1973）。然而，两个立方晶格的应用——一个用于对相邻原子中心进行分组，另一个用于对原子的相邻表面点进行分组——通过避免冗余距离检查，导致中央处理单元（CPU）时间消耗大幅减少。这对于紧凑的构象最为明显。例如，计算牛胰蛋白酶抑制剂晶体构象的溶剂可及表面积（Brookhaven 蛋白质数据库的条目 4PTI，所有 454 个非氢原子的 362 点球体）只需不到 1 秒（在 SGI 4D/480 的单个 R3000 处理器上，大约 5 MFLOP）。 DCLM 不依赖于所应用的球形点分布。讨论了单位球面镶嵌的质量。我们提出了基于二十面体和十二面体的新细分方法，该方法在整个频率范围内实现了最长与最短弧的持续低比率。 DCLM 是首选方法，特别是对于大分子复合物和高点密度。其速度与作者已知的最快技术进行了比较，发现它更为优越，特别是在考虑到较小的内存需求和算法的灵活性时。程序文本可根据要求获取。 (C) 1995 年，约翰·威利父子公司 (John Wiley and Sons, Inc.)
The double cubic lattice method (DCLM) is an accurate and rapid approach for computing numerically molecular surface areas (such as the solvent accessible or van der Waals surface) and the volume and compactness of molecular assemblies and for generating dot surfaces. The algorithm has no special memory requirements and can be easily implemented. The computation speed is extremely high, making interactive calculation of surfaces, volumes, and dot surfaces for systems of 1000 and more atoms possible on single-processor workstations. The algorithm can be easily parallelized. The DCLM is an algorithmic variant of the approach proposed by Shrake and Rupley (J. Mol. Biol., 79, 351-371, 1973). However, the application of two cubic lattices-one for grouping neighboring atomic centers and the other for grouping neighboring surface dots of an atom-results in a drastic reduction of central processing unit (CPU) time consumption by avoiding redundant distance checks. This is most noticeable for compact conformations. For instance, the calculation of the solvent accessible surface area of the crystal conformation of bovine pancreatic trypsin inhibitor (entry 4PTI of the Brookhaven Protein Data Bank, 362-point sphere for all 454 nonhydrogen atoms) takes less than 1 second (on a single R3000 processor of an SGI 4D/480, about 5 MFLOP). The DCLM does not depend on the spherical point distribution applied. The quality of unit sphere tesselations is discussed. We propose new ways of subdivision based on the icosahedron and dodecahedron, which achieve constantly low ratios of longest to shortest arcs over the whole frequency range. The DCLM is the method of choice, especially for large molecular complexes and high point densities. Its speed has been compared to the fastest techniques known to the authors, and it was found to be superior, especially when also taking into account the small memory requirement and the flexibility of the algorithm. The program text may be obtained on request. (C) 1995 by John Wiley and Sons, Inc.