TheBio3Dpackages for structural bioinformatics
TheBio3Dpackages for structural bioinformatics
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DOI：
10.1002/pro.3923
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发表时间：
2020-08-17
期刊：
影响因子：
8
通讯作者：
Yao, Xin-Qiu
中科院分区：
文献类型：
--
作者：
Grant, Barry J.;Skjaerven, Lars;Yao, Xin-Qiu
Bio3D是一个用于分析生物分子序列、结构和动力学的R软件包家族。主要功能包括生物分子数据库检索、序列和结构保守分析、集合正态分析、蛋白质结构和相关网络分析、主成分分析以及相关的多变量分析方法。在这里，我们回顾了最近的封装发展，包括一种新的潜在的分离到单独的封装来进行不同的分析，并介绍了一种新的结构分析方法，称为集成差距矩阵分析（eDDM）。eDDM方法计算和比较大量同源原子结构的原子距离矩阵，以帮助确定特定功能过程的剩余决定因素。详细介绍了eDDM工作流程以及一个大型蛋白质家族的示例应用程序。作为Bio3D家族的新成员，Bio3D-eddm包支持实验和理论模拟生成的结构，与其他方法集成用于解剖序列-结构-功能关系，并且可以以高度自动化和可重复的方式使用。Bio3D作为一组独立于平台的开源R包发布，可从：
Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis namedensemble difference distance matrix analysis(eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D-eddm package supports both experimental and theoretical simulation-generated structures, is integrated with other methods for dissecting sequence-structure-function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: .