Pharmacoinformatics group, Research Programme on Biomedical Informatics (GRIB), Universitat Pompeu Fabra (UPF)-Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain, Department of Physics, Tampere University of Technology, Tampere, Finland and Institute of Biomedical Engineering, National Research Council of Italy (ISIB-CNR), Padua, Italy.
Bioinformatics. 2014 May 15;30(10):1478-80. doi: 10.1093/bioinformatics/btu037. Epub 2014 Jan 21.
Computer simulations are giving way to more complex and accurate studies of biological membranes by molecular dynamics (MD) simulations. The analysis of MD trajectories comprises the biophysical characterization of membrane properties or the study of protein-lipid interactions and dynamics. However, there is a lack of automated tools to analyse MD simulations of complex membrane or membrane-protein systems. Here we present MEMBPLUGIN, a plugin for the Visual Molecular Dynamics package that provides algorithms to measure a host of essential biophysical properties in simulated membranes. MEMBPLUGIN features are accessible both through a user-friendly graphical interface and as command-line procedures to be invoked in analysis scripts.
MEMBPLUGIN is a VMD extension written in Tcl. Multi-platform source code, documentation and tutorials are freely available at http://membplugin.sourceforge.net.
toni.giorgino@isib.cnr.it or jana.selent@upf.edu
Supplementary data are available at Bioinformatics online.
计算机模拟正让位于更复杂、更精确的基于分子动力学 (MD) 模拟的生物膜研究。MD 轨迹分析包括对膜性质的生物物理特征分析或对蛋白-脂相互作用和动力学的研究。然而，目前缺乏用于分析复杂膜或膜蛋白系统 MD 模拟的自动化工具。在此，我们介绍 MEMBPLUGIN，这是一个适用于 Visual Molecular Dynamics 包的插件，它提供了用于测量模拟膜中一系列重要生物物理性质的算法。MEMBPLUGIN 的功能既可以通过用户友好的图形界面访问，也可以通过命令行过程在分析脚本中调用。
MEMBPLUGIN 是一个用 Tcl 编写的 VMD 扩展。多平台的源代码、文档和教程可在 http://membplugin.sourceforge.net 免费获取。
toni.giorgino@isib.cnr.it 或 jana.selent@upf.edu
补充数据可在 Bioinformatics 在线获取。
