CAMERRA: An analysis tool for the computation of conformational dynamics by evaluating residue-residue associations
CAMERRA: An analysis tool for the computation of conformational dynamics by evaluating residue-residue associations
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DOI：
10.1002/jcc.25192
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发表时间：
2018-07-30
影响因子：
3
通讯作者：
Shen, Tongye
中科院分区：
文献类型：
--
作者：
Johnson, Quentin R.;Lindsay, Richard J.;Shen, Tongye
提出了一种通过残基-残基接触的相关分析从生物分子构象集合中提取优势运动的计算方法。该算法首先将结构信息呈现为接触矩阵，然后根据所选择的一组动态接触的相关动力学构造集体模式。相关程序可以桥接结果，以便使用图形软件进一步可视化。该方法的目的是从接触的角度对生物聚合物的构象进行分析。它可以通过模拟快照的统计分析，帮助系统地揭示存在于蛋白质和生物聚合物系统中的构象开关机制。与笛卡尔坐标的传统相关分析（如距离协方差分析和笛卡尔主成分分析）相比，该程序还提供了一种替代方法来定位基本的集体运动。在这里，我们以逐步的方式详细介绍了该算法，并评论了该方法在解码变构机制方面的重要性。(c) 2018 Wiley期刊公司
A computational method which extracts the dominant motions from an ensemble of biomolecular conformations via a correlation analysis of residue-residue contacts is presented. The algorithm first renders the structural information into contact matrices, then constructs the collective modes based on the correlated dynamics of a selected set of dynamic contacts. Associated programs can bridge the results for further visualization using graphics software. The aim of this method is to provide an analysis of conformations of biopolymers from the contact viewpoint. It may assist a systematical uncovering of conformational switching mechanisms existing in proteins and biopolymer systems in general by statistical analysis of simulation snapshots. In contrast to conventional correlation analyses of Cartesian coordinates (such as distance covariance analysis and Cartesian principal component analysis), this program also provides an alternative way to locate essential collective motions in general. Herein, we detail the algorithm in a stepwise manner and comment on the importance of the method as applied to decoding allosteric mechanisms. (c) 2018 Wiley Periodicals, Inc.