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Bio3D Package for Biological Structure Analysis

Utilities to analyze, process, organize and explore biomolecular structure, sequence and dynamics data.

Features

Features include the ability to read and write structure, sequence and dynamic trajectory data, perform database searches, atom summaries, atom selection, re-orientation, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis (NMA), correlation network analysis (CNA) and principal component analysis (PCA).

In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the main Bio3D website for more background information.

Installing Bio3D

For the majority of users we recommend the use of the last stable release available from CRAN and the main Bio3D website. To install from within R issue the command:

#!r
install.packages("bio3d", dependencies=TRUE)

The development version is available from our bitbucket repository and typically contains new functions and bug fixes that have not yet been incorporated into the latest stable release. The simplest method for development version installation is to use the R function install_bitbucket() from the devtools package:

#!r
install.packages("devtools")
library(devtools)
install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/")

Alternative installation methods and additional instructions are posted to the wiki section of our bitbucket repository.

Installing the bio3d.core package of the Bio3D family

Since 2020, we have started a new way to develop and implement Bio3D: Instead of maintaining a single R package (bio3d), we put main modules into separate packages. The bio3d.core package provides functionality for data processing and basic sequence, structure and dynamics analyses. This package is required for other packages of the Bio3D family (See below). To install it, use the install_bitbucket() function from the devtools package:

#!r
library(devtools)
install_bitbucket("Grantlab/bio3d/bio3d-core", "core")

Other packages in the Bio3D family

With growing functionality in Bio3D we have decided to implement larger Bio3D modules into separate packages:

• Bio3D-web for online interactive analysis of protein structure ensembles
• Bio3D-nma for Normal Mode Analysis (NMA) of protein structures and ensembles
• Bio3D-cna for Correlation Network Analysis (CNA) for protein structure ensembles
• Bio3D-eddm for Distances matrix analysis for the identification of significant conformational changes underling functional processes
• Bio3D-gesostas for the identification of geometrically stable domains in biomolecules
• Bio3D-view for interactive visualization of structures in R

Current ongoing projects entails:

• Bio3D-mmtf [In development]
• Bio3D-amber [In development]
• Bio3D-muscle [In development]
• Bio3D-cheminf
• Bio3D-dcna

Contributing to Bio3D

We are always interested in adding additional functionality to Bio3D. If you have ideas, suggestions or code that you would like to distribute as part of this package, please contact us (see below). You are also encouraged to contribute your code or issues directly to this repository for incorporation into the development version of the package. For details on how to do this please see the developer wiki.

Contact

You are welcome to:

• Submit suggestions and bug-reports at: https://bitbucket.org/Grantlab/bio3d/issues
• Send a pull request on: https://bitbucket.org/Grantlab/bio3d/pull-requests
• Compose a friendly e-mail to: bjgrant@ucsd.edu