R: Biological Structure Analysis

bio3d-package {bio3d} | R Documentation

## Biological Structure Analysis

### Description

Utilities for the analysis of protein structure and sequence data.

### Details

Package: | bio3d
Type: | Package
Version: | 2.3-4
Date: | 2018-04-01
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.).

### 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(s)

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

    ## Not run:
    ##-- 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

    ## End(Not run)

[Package bio3d version 2.3-4 Index]