---
title: "bio3d Vignettes"
date: "Sep 22 2016"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteIndexEntry{bio3d Vignettes}
  \usepackage[utf8]{inputenc}
---

We distribute a number of extended **Bio3D vignettes** that provide worked examples of using Bio3D to perform a particular type of structural bioinformatics analysis. An updated list of these can be found on-line (http://thegrantlab.org/bio3d/tutorials).

At the time of writing these include:

* Installing Bio3D ( PDF (http://thegrantlab.org/bio3d/phocadownload/vignettes/Bio3D_install.pdf) | HTML (http://thegrantlab.org/bio3d/tutorials/installing-bio3d))
* Getting started with Bio3D ( PDF | HTML (http://thegrantlab.org/bio3d/user-guide) )
* PDB structure manipulation and analysis with Bio3D ( PDF (http://thegrantlab.org/bio3d/phocadownload/vignettes/Bio3D_pdb.pdf) | HTML (http://thegrantlab.org/bio3d/tutorials/structure-analysis))
* Comparative sequence and structure analysis with Bio3D ( PDF (http://thegrantlab.org/bio3d/phocadownload/vignettes/Bio3D_pca.pdf) | HTML (http://thegrantlab.org/bio3d/tutorials/principal-component-analysis))
* Beginning trajectory analysis with Bio3D ( PDF (http://thegrantlab.org/bio3d/phocadownload/vignettes/Bio3D_md.pdf) | HTML (http://thegrantlab.org/bio3d/tutorials/trajectory-analysis))
* Enhanced methods for Normal Mode Analysis with Bio3D ( PDF (http://thegrantlab.org/bio3d/phocadownload/vignettes/Bio3D_nma.pdf) | HTML (http://thegrantlab.org/bio3d/tutorials/normal-mode-analysis))
* Ensemble NMA of E.coli DHFR structures ( PDF (http://thegrantlab.org/bio3d/phocadownload/vignettes/Bio3D_nma-dhfr-partI.pdf) | HTML (http://thegrantlab.org/bio3d/tutorials/ensemble-nma-part-1) )
* Ensemble NMA across multiple species of DHFR ( PDF (http://thegrantlab.org/bio3d/phocadownload/vignettes/Bio3D_nma-dhfr-partII.pdf) | HTML (http://thegrantlab.org/bio3d/tutorials/ensemble-nma-part-2) )
* Correlation network analysis with Bio3D ( PDF (http://thegrantlab.org/bio3d/phocadownload/vignettes/Bio3D_cna-transducin.pdf) | HTML (http://thegrantlab.org/bio3d/tutorials/ensemble-nma-part-1/81-vignettes/87-correlation-network-analysis-with-bio3d) )
* Protein structure network analysis with Bio3D ( PDF (http://thegrantlab.org/bio3d/phocadownload/vignettes/cna_vignette.pdf) | HTML (http://thegrantlab.org/bio3d/tutorials/protein-structure-networks) )
* Online protein structure analysis with the Bio3D WebApp ( PDF (http://thegrantlab.org/bio3d/phocadownload/vignettes/PCA-WebApp.pdf) | HTML )
* Online Normal Mode Analysis with Bio3D WebApps ( PDF (http://thegrantlab.org/bio3d/phocadownload/vignettes/NMA-WebApp.pdf) | HTML )

There is also extensive on-line documentation (http://thegrantlab.org/bio3d/html/index.html) with worked examples (and their output) for all functions and a package manual (http://thegrantlab.org/bio3d/bio3d.pdf) (in PDF format) that is a concatenation of each functions documentation (without example output).

Note that for information on Bio3D development status or to report a bug, please refer to: https://bitbucket.org/Grantlab/bio3d
