The Bio3D package for structural bioinformatics consists of sets of functions for:
- sequence analysis,
- structure analysis,
- simulation analysis,
- normal mode analysis,
- correlation network analysis,
- format conversion and data manipulation, and
- graphics and visualization..
Major functions are listed below with links to further documentation that includes example code and results.
Note that you can also get help on any particular function by using the command
help(read.pdb)) and directly execute the example code for a given function with the command
example(function) from within R itself.
We also distribute a number of extended Bio3D vignettes that provide worked examples of using Bio3D to perform a particular type of analysis. Currently available vignettes include:
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