bio3d: Biological Structure Analysis

Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. 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 URLs below for more information.

Version: 2.2-3
Depends: R (≥ 3.1.0)
Imports: parallel, grid, graphics, grDevices, stats, utils
Suggests: XML, RCurl, lattice, ncdf, igraph, bigmemory, knitr, testthat (≥ 0.9.1)
Published: 2015-09-04
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
Maintainer: Barry Grant <bjgrant at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
Citation: bio3d citation info
Materials: README NEWS
CRAN checks: bio3d results


Reference manual: bio3d.pdf
Vignettes: bio3d Vignettes
Package source: bio3d_2.2-3.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X Snow Leopard binaries: r-release: bio3d_2.2-3.tgz, r-oldrel: bio3d_2.2-2.tgz
OS X Mavericks binaries: r-release: bio3d_2.2-3.tgz
Old sources: bio3d archive