bio3d Vignettes

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/