MD-TASK：一个用于分析分子动力学轨迹的软件套件。
MD-TASK: a software suite for analyzing molecular dynamics trajectories.
作者信息
Brown David K, Penkler David L, Sheik Amamuddy Olivier, Ross Caroline, Atilgan Ali Rana, Atilgan Canan, Tastan Bishop Özlem
机构信息
Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa.
Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla 34956, Istanbul, Turkey.
出版信息
Bioinformatics. 2017 Sep 1;33(17):2768-2771. doi: 10.1093/bioinformatics/btx349.
SUMMARY
Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energy measures have been used to analyze MD simulations. Here, we present MD-TASK, a novel software suite that employs graph theory techniques, perturbation response scanning, and dynamic cross-correlation to provide unique ways for analyzing MD trajectories.
AVAILABILITY AND IMPLEMENTATION
MD-TASK has been open-sourced and is available for download from https://github.com/RUBi-ZA/MD-TASK , implemented in Python and supported on Linux/Unix.
CONTACT
摘要
分子动力学（MD）可确定生物大分子的原子在类细胞环境中的物理运动，是结构生物信息学中的一种重要方法。传统上，诸如均方根偏差、均方根波动、回转半径和各种能量度量等测量方法已被用于分析分子动力学模拟。在此，我们展示了MD-TASK，这是一个新颖的软件套件，它采用图论技术、微扰响应扫描和动态互相关来提供分析分子动力学轨迹的独特方法。
可用性和实现方式
MD-TASK已开源，可从https://github.com/RUBi-ZA/MD-TASK下载，用Python实现并支持在Linux/Unix系统上运行。
联系方式
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