MOLE:: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels
MOLE:: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels
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DOI：
10.1016/j.str.2007.10.007
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发表时间：
2007-11-01
期刊：
影响因子：
5.7
通讯作者：
Otyepka, Michal
中科院分区：
文献类型：
--
作者：
Petrek, Martin;Kosinova, Pavlina;Otyepka, Michal
我们开发了一种算法，“MOLE”，用于快速，全自动定位和表征分子通道，隧道和孔隙。这个算法已经在互联网上免费提供（http://mole.chemi）。市政。cz/)，克服了最近开发的CAVER软件的许多缺点和局限性。我们的MOLE算法的核心是Dijkstra路径搜索算法，该算法应用于Voronoi网格。对多种生物分子系统的测试，包括革兰西啶、乙酰胆碱酯酶、细胞色素P450、钾通道、DNA四联体、核酶和大型核糖体亚基，已经证明MOLE算法表现良好。因此，MOLE是探索大分子通道、复杂通道网络和分子动力学轨迹的强大工具，其中需要分析大量快照。
We have developed an algorithm, "MOLE," for the rapid, fully automated location and characterization of molecular channels, tunnels, and pores. This algorithm has been made freely available on the Internet (http://mole.chemi. muni.cz/) and overcomes many of the shortcomings and limitations of the recently developed CAVER software. The core of our MOLE algorithm is a Dijkstra's path search algorithm, which is applied to a Voronoi mesh. Tests on a wide variety of biomolecular systems including gramicidine, acetylcholinesterase, cytochromes P450, potassium channels, DNA quadruplexes, ribozymes, and the large ribosomal subunit have demonstrated that the MOLE algorithm performs well. MOLE is thus a powerful tool for exploring large molecular channels, complex networks of channels, and molecular dynamics trajectories in which analysis of a large number of snapshots is required.