MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
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DOI：
10.1016/j.bpj.2015.08.015
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发表时间：
2015-10-20
影响因子：
3.4
通讯作者：
Pande, Vijay S.
中科院分区：
文献类型：
--
作者：
McGibbon, Robert T.;Beauchamp, Kyle A.;Pande, Vijay S.
随着分子动力学（MD）模拟继续发展成为研究复杂生物分子系统的强大计算工具，用于分析这些模拟的灵活且易于使用的软件工具的必要性正在增长。我们已经开发了MDTraj，一个现代化的，轻量级的，快速的软件包，用于分析MD模拟。MDTraj以各种常用格式读取和写入轨迹数据。它提供了大量的轨迹分析功能，包括最小均方根偏差计算，二级结构分配，和提取共同的顺序参数。该软件包非常注重与更广泛的科学Python生态系统的互操作性，弥合了MD数据与Python中快速增长的行业标准统计分析和可视化工具之间的差距。MDTraj是一个功能强大且用户友好的软件包，它简化了MD数据的分析，并将这些数据集与Python中的现代交互式数据科学软件生态系统连接起来。
As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.