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.

Documentation

Manual: bio3d.pdf
Vignette: bio3d Vignettes

Maintainer: Barry Grant <bjgrant at umich.edu>

Author(s): Barry Grant*, Xin-Qiu Yao*, Lars Skjaerven*, Julien Ide*

Install package and any missing dependencies by running this line in your R console:

install.packages("bio3d")

Depends R (>= 3.1.0)
Imports Rcpp, parallel, grid, graphics, grDevices, stats, utils
Suggests XML, RCurl, lattice, ncdf4, igraph, bigmemory, knitr, testthat(>=0.9.1), httr
Enhances
Linking to Rcpp
Reverse
depends
Rknots
Reverse
imports
aLFQ, CampaR1, COUSCOus
Reverse
suggests
Reverse
enhances
Reverse
linking to

Package bio3d
Materials
URL http://thegrantlab.org/bio3d/ http://bitbucket.org/Grantlab/bio3d
Task Views
Version 2.3-2
Published 2017-06-14
License GPL (>= 2)
BugReports
SystemRequirements
NeedsCompilation yes
Citation
CRAN checks bio3d check results
Package source bio3d_2.3-2.tar.gz