Bio3D v2.3


We are happy to announce the release of version 2.3 of Bio3D. This release contains several new functions and important improvements to existing code and documentation.

Explore What's New

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 2 license. Please see the Download page for installation instructions. 

Features

  • 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

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 ) 

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 In press.
( Abstract | PubMed | PDF )

What's new

Bio3D version 2.3

We are excited to announce the release of version 2.3 of Bio3D. This release contains several new functions and important improvements to existing code and documentation.

Read more ...

Bio3D version 2.2

We are excited to announce the release of version 2.2 of Bio3D. This release contains several new functions and important improvements to existing code and documentation.

Note important bugfix related to function atom.select() released with version 2.2-2 (March 2 2015).

Read more ...

Core developers

Barry Grant
University of Michigan

Xinqiu Yao
University of Michigan

Lars Skjærven
University of Bergen

Julien Ide
University of Mons

Developer links

Bitbucket activity

  • BUGFIX: wrong indexing in find_relevant_biounit() causing crashes for some PDB IDs
    12 September 2018, 9:38 pm Read more...
  • ENHANCEMENT: separate part of code from play.biounit() to make find_relevant_biounit() - TO DO: - with value=TRUE, chains will be reordered by putting relevant chains on top, while this chain reordering information is missing with value=FALSE.
    10 September 2018, 9:27 pm Read more...
  • minor updates to docker files
    10 September 2018, 6:21 pm Read more...
  • BUGFIX: writing 'aln.fa' error in pdbaln() call for bioassembly - Also modified play.biounit() to return a full length (equal to length(pdbs)) vector, where PDBs having no biounit returned are labeled by 'NA'. - In addition, play.biounit() returns both relevant biounit files and corresponding indices of these biounits with respect to all valid biounits in PDB files.
    10 September 2018, 4:24 pm Read more...
  • bugfix in closing progressbars
    10 September 2018, 3:24 pm Read more...