Biological Structure Analysis — bio3d-package • Bio3D

Utilities for the analysis of protein structure and sequence data.

Details

Package:	bio3d
Type:	Package
Version:	2.4-1
Date:	2020-01-20
License:	GPL version 2 or newer
URL:	http://thegrantlab.org/bio3d/

Features include the ability to read and write structure (read.pdb, write.pdb, read.fasta.pdb), sequence (read.fasta, write.fasta) and dynamics trajectory data (read.dcd, read.ncdf, write.ncdf).

Perform sequence and structure database searches (blast.pdb, hmmer), atom summaries (summary.pdb), atom selection (atom.select), alignment (pdbaln, seqaln, mustang) superposition (rot.lsq, fit.xyz), pdbfit), rigid core identification (core.find, plot.core, fit.xyz), dynamic domain analysis (geostas), torsion/dihedral analysis (torsion.pdb, torsion.xyz), clustering (via hclust), principal component analysis (pca.xyz, pca.pdbs, pca.tor, plot.pca, plot.pca.loadings, mktrj.pca), dynamical cross-correlation analysis (dccm, plot.dccm) and correlation network analysis (cna, plot.cna, cnapath) of structure data.

Perform conservation analysis of sequence (seqaln, conserv, seqidentity, entropy, consensus) and structural (pdbaln, rmsd, rmsf, core.find) data.

Perform normal mode analysis (nma, build.hessian), ensemble normal mode analysis (nma.pdbs), mode comparison (rmsip) and (overlap), atomic fluctuation prediction (fluct.nma), cross-correlation analysis (dccm.nma), cross-correlation visualization (pymol.dccm), deformation analysis (deformation.nma), and mode visualization (pymol.modes, mktrj.nma).

In addition, various utility functions are provided to facilitate manipulation and analysis of biological sequence and structural data (e.g. get.pdb, get.seq, aa123, aa321, pdbseq, aln2html, atom.select, rot.lsq, fit.xyz, is.gap, gap.inspect, orient.pdb, pairwise, plot.bio3d, plot.nma, plot.blast, biounit, etc.).

Note

The latest version, package vignettes and documentation with worked example outputs can be obtained from the bio3d website:
http://thegrantlab.org/bio3d/.
http://thegrantlab.org/bio3d/html/.
http://bitbucket.org/Grantlab/bio3d.

Author

Barry Grant <bjgrant@ucsd.edu> Xin-Qiu Yao <xinqiu.yao@gmail.com> Lars Skjaerven <larsss@gmail.com> Julien Ide <julien.ide.fr@gmail.com>

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399.

Examples

help(package="bio3d")     # list the functions within the package
#lbio3d()                  # list bio3d function names only

## Or visit:
##   http://thegrantlab.org/bio3d/html/

## See the individual functions for further documentation and examples, e.g.
#help(read.pdb)

## Or online:
##    http://thegrantlab.org/bio3d/html/read.pdb.html

if (FALSE) {
##-- See the list of Bio3D demos
demo(package="bio3d")

## Try some out, e.g:
demo(pdb) # PDB Reading, Manipulation, Searching and Alignment
demo(pca) # Principal Component Analysis
demo(md)  # Molecular Dynamics Trajectory Analysis
demo(nma) # Normal Mode Analysis

## See package vignettes and tutorals online:
##   http://thegrantlab.org/bio3d/tutorials
}