bio3d Vignettes
In bio3d: Biological Structure Analysis

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.

At the time of writing these include:

Installing Bio3D
Getting started with Bio3D
PDB structure manipulation and analysis with Bio3D
Beginning trajectory analysis with Bio3D
Enhanced methods for Normal Mode Analysis with Bio3D
Comparative sequence and structure analysis with Bio3D
Ensemble NMA of E.coli DHFR structures
Ensemble NMA across multiple species of DHFR
Protein structure network analysis with Bio3D
Introduction to Ensemble Difference Distance Matrix (eDDM) Analysis
Online protein structure analysis with the Bio3D WebApp ( PDF)
Online Normal Mode Analysis with Bio3D WebApps ( PDF | HTML )

There is also extensive on-line documentation with worked examples (and their output) for all functions and a package manual (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/