Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories
Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories
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DOI：
10.1002/jcc.23381
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发表时间：
2013-10-05
影响因子：
3
通讯作者：
Glykos, Nicholas M.
中科院分区：
文献类型：
--
作者：
Koukos, Panagiotis I.;Glykos, Nicholas M.
我们报告了grcarma的可用性，grcarma是一种编码全自动任务集的程序，旨在简化生物大分子分子动力学轨迹的分析。它是一个跨平台的，基于Perl/ tk的程序前端，旨在满足新手和专家用户的需求，同时保持用户友好和直观的设计。重点介绍了基于二面体和笛卡尔主成分分析的结构簇提取、二次结构分析、均方根偏差（RMSD）矩阵的计算和显示、熵的计算、方差-协方差矩阵的计算和分析、原生接触比例的计算等繁琐任务的自动化。该程序是免费的开源软件，可立即下载。(c) 2013 Wiley Periodicals, Inc.；
We report the availability of grcarma, a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories of biological macromolecules. It is a cross-platform, Perl/Tk-based front-end to the program carma and is designed to facilitate the needs of the novice as well as those of the expert user, while at the same time maintaining a user-friendly and intuitive design. Particular emphasis was given to the automation of several tedious tasks, such as extraction of clusters of structures based on dihedral and Cartesian principal component analysis, secondary structure analysis, calculation and display of root-mean-square deviation (RMSD) matrices, calculation of entropy, calculation and analysis of variance-covariance matrices, calculation of the fraction of native contacts, etc. The program is free-open source software available immediately for download. (c) 2013 Wiley Periodicals, Inc.