Utilities for the analysis of protein structure and sequence data.
| Package: |
| bio3d |
| Type: |
| Package |
| Version: |
| 2.3-0 |
| Date: |
| 2016-09-15 |
| 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, lmi, 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.).
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.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399.
## <strong>Not run</strong>: # help(package="bio3d") # list the functions within the package # ## <strong>End(Not run)</strong> #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 ##-- See the list of Bio3D demos ## <strong>Not run</strong>: # demo(package="bio3d") # ## <strong>End(Not run)</strong> ## Try some out, e.g: ## <strong>Not run</strong>: # demo(pdb) # PDB Reading, Manipulation, Searching and Alignment # ## <strong>End(Not run)</strong> ## <strong>Not run</strong>: # demo(pca) # Principal Component Analysis # ## <strong>End(Not run)</strong> ## <strong>Not run</strong>: # demo(md) # Molecular Dynamics Trajectory Analysis # ## <strong>End(Not run)</strong> ## <strong>Not run</strong>: # demo(nma) # Normal Mode Analysis # ## <strong>End(Not run)</strong> ## See package vignettes and tutorals online: ## http://thegrantlab.org/bio3d/tutorials