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: 2.4-4
Depends: R (≥ 3.1.0)
Imports: Rcpp, parallel, grid, graphics, grDevices, stats, utils
LinkingTo: Rcpp
Suggests: XML, RCurl, lattice, ncdf4, igraph, bigmemory, knitr, rmarkdown, testthat (≥ 0.9.1), httr, msa, Biostrings
Published: 2022-10-26
DOI: 10.32614/CRAN.package.bio3d
Author: Barry Grant [aut, cre], Xin-Qiu Yao [aut], Lars Skjaerven [aut], Julien Ide [aut]
Maintainer: Barry Grant <bjgrant at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Citation: bio3d citation info
Materials: README NEWS
In views: Omics
CRAN checks: bio3d results


Reference manual: bio3d.pdf
Vignettes: bio3d Vignettes


Package source: bio3d_2.4-4.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): bio3d_2.4-4.tgz, r-oldrel (arm64): bio3d_2.4-4.tgz, r-release (x86_64): bio3d_2.4-4.tgz, r-oldrel (x86_64): bio3d_2.4-4.tgz
Old sources: bio3d archive

Reverse dependencies:

Reverse imports: aLFQ, compas, EnvNJ, ptm, r3dmol, rPDBapi
Reverse suggests: AlphaMissenseR, factR


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