Kim Jae-Kwan, Cho Youngsong, Laskowski Roman A, Ryu Seong Eon, Sugihara Kokichi, Kim Deok-Soo
Vorononi Diagram Research Center, Hanyang University, Korea.
Proteins. 2014 Sep;82(9):1829-49. doi: 10.1002/prot.24537. Epub 2014 Mar 20.
Molecular external structure is important for molecular function, with voids on the surface and interior being one of the most important features. Hence, recognition of molecular voids and accurate computation of their geometrical properties, such as volume, area and topology, are crucial, yet most popular algorithms are based on the crude use of sampling points and thus are approximations even with a significant amount of computation. In this article, we propose an analytic approach to the problem using the Voronoi diagram of atoms and the beta-complex. The correctness and efficiency of the proposed algorithm is mathematically proved and experimentally verified. The benchmark test clearly shows the superiority of BetaVoid to two popular programs: VOIDOO and CASTp. The proposed algorithm is implemented in the BetaVoid program which is freely available at the Voronoi Diagram Research Center (http://voronoi.hanyang.ac.kr).
分子外部结构对分子功能很重要，表面和内部的空隙是最重要的特征之一。因此，识别分子空隙并准确计算其几何性质，如体积、面积和拓扑结构，至关重要，但大多数流行算法都基于对采样点的粗略使用，因此即使进行大量计算也是近似值。在本文中，我们提出了一种使用原子的Voronoi图和β-复合体来解决该问题的解析方法。所提算法的正确性和效率在数学上得到了证明，并通过实验进行了验证。基准测试清楚地表明了BetaVoid相对于两个流行程序VOIDOO和CASTp的优越性。所提算法在BetaVoid程序中实现，该程序可在Voronoi图研究中心（http://voronoi.hanyang.ac.kr）免费获取。
