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 named ensemble 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: http://thegrantlab.org/bio3d/.

中文翻译：

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用于结构生物信息学的 Bio3D 软件包。

Bio3D 是一系列用于分析生物分子序列、结构和动力学的 R 包。主要功能包括生物分子数据库搜索和检索、序列和结构守恒分析、集合正态模式分析、蛋白质结构和相关网络分析、主成分和相关的多元分析方法。在这里，我们回顾了最近的包发展，包括一个新的基础分离到单独的包以进行不同的分析，并介绍了一种名为集成差异距离矩阵分析的结构分析新方法(eDDM)。eDDM 方法计算和比较大量同源原子结构的原子距离矩阵，以帮助识别特定功能过程背后的残基决定因素。详细介绍了 eDDM 工作流程以及大型蛋白质家族的示例应用。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，与其他分析序列-结构-功能关系的方法相结合，并且可以以高度自动化和可重复的方式使用。Bio3D 作为一组集成的独立于平台的开源 R 包分发，可从以下网址获得：http://thegrantlab.org/bio3d/。