Laurent Benoist, Chavent Matthieu, Cragnolini Tristan, Dahl Anna Caroline E, Pasquali Samuela, Derreumaux Philippe, Sansom Mark S P, Baaden Marc
Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
Bioinformatics. 2015 May 1;31(9):1478-80. doi: 10.1093/bioinformatics/btu822. Epub 2014 Dec 12.
The volume of an internal protein pocket is fundamental to ligand accessibility. Few programs that compute such volumes manage dynamic data from molecular dynamics (MD) simulations. Limited performance often prohibits analysis of large datasets. We present Epock, an efficient command-line tool that calculates pocket volumes from MD trajectories. A plugin for the VMD program provides a graphical user interface to facilitate input creation, run Epock and analyse the results.
Epock C++ source code, Python analysis scripts, VMD Tcl plugin, documentation and installation instructions are freely available at http://epock.bitbucket.org.
benoist.laurent@gmail.com or baaden@smplinux.de
Supplementary data are available at Bioinformatics online.
内部蛋白质口袋的体积对于配体可及性至关重要。很少有计算此类体积的程序能够处理来自分子动力学（MD）模拟的动态数据。性能受限常常阻碍对大型数据集的分析。我们展示了Epock，这是一个从MD轨迹计算口袋体积的高效命令行工具。VMD程序的一个插件提供了图形用户界面，以方便输入创建、运行Epock并分析结果。
Epock C++ 源代码、Python分析脚本、VMD Tcl插件、文档及安装说明可在http://epock.bitbucket.org免费获取。
benoist.laurent@gmail.com或baaden@smplinux.de
补充数据可在《生物信息学》在线获取。
Zotero 插件