Overview

Bio3D is an R package containing utilities for the analysis of protein structure, sequence and trajectory data.

It is currently distributed as platform independent source code under the GPL version 3 license. Major features include:

• The ability to read, write and process biomolecular structure, sequence and dynamics trajectory data. >> more
• Perform atom selection, alignment and superposition, rigid core identification, dynamic domain analysis, conformational clustering, correlation network analysis, torsion analysis, distance matrix analysis and principal component analysis of structure data. >> more
• Perform ensemble normal mode analysis on large structure sets to explore evolutionary dynamics and structure dependent protein flexibility. >> more
• Perform conservation analysis of sequence and structural data. >> more
• Integration of major protein structure and sequence databases and associated search tools. >> more
• 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. >> more

Quick Install

On all platforms (Mac, Linux, and PC) open R (version 3.1.0 or higher) and use the function install.packages("bio3d") at the R command prompt to install the package from your local CRAN site:

install.packages("bio3d", dependencies=TRUE)

For more detailed installation and setup instructions please see the Installing Bio3D page.

Getting Started

First time users may find our getting started guide helpful.

We also distribute a number of extended Bio3D vignettes that provide worked examples of using Bio3D to perform a particular type of analysis. There is also a package manual (in PDF format) that is a concatenation of each functions documentation.

Development

For information on current and future development of Bio3D, see the Bio3D project on BitBucket. Details of recent package changes and reported issues can also be found on BitBucket.

Citing Bio3D

Bio3D: An R package for the comparative analysis of protein structures.
Grant, Rodrigues, ElSawy, McCammon, Caves, (2006) Bioinformatics 22, 2695-2696
( Abstract | PubMed | PDF | BibTeX )

Integrating protein structural dynamics and evolutionary analysis with Bio3D. Skjærven, Yao, Scarabelli, Grant, (2014) BMC Bioinformatics 15, 399
( Abstract | PubMed | PDF )

Online interactive analysis of protein structure ensembles with Bio3D-web. Skjærven, Jariwala, Yao, Grant, (2016) Bioinformatics 32, 3510-3512
( Abstract | PubMed | PDF )

The Bio3D packages for structural bioinformatics.
Grant, Skjærven, Yao (2020) Protein Science, In press.
( Abstract | PubMed | PDF )