Lot’s of structural bioinformatics analysis. Major features include the ability to read and write biomolecular structure, sequence and dynamic trajectory data, query and search online sequence and structure databases, perform atom selection, re-orientation, superposition, rigid core identification, clustering, distance matrix analysis, alignment, conservation analysis, normal mode analysis, principal component analysis, and many, many other common sequence and structural analysis tasks.
Bio3D aims to leverage the extensive graphical and statistical capabilities of the R environment <www.r-project.org> and thus provide a useful integrated framework for the exploratory interactive analysis of biomolecular sequence and structure data.
To get the most out of Bio3D you should be quite familiar with basic R usage. Some newcomers to R find this a steep learning curve. However, once you have mastered basic operations with vectors and matrices in R you should feel confident about getting stuck into using the Bio3D package.
There are numerous on–line resources that can help you get started using R. A number of these can be found from the main R website at http://www.r-project.org. We particularly like the following:
There are also several books providing valuable skills in R:
R and Bio3D can be installed on all commonly used architectures and operative systems such as Linux, Mac OSX, and Windows. The Bio3D Installation guide provides a thorough description of the process, which can be summarized into one line of code from the R console:
From the main Bio3D website you can find the latest version of the package, full documentation and extensive vignettes and tutorials.
We provide a Q&A and issue tracker system at our Bitbucket site: https://bitbucket.org/Grantlab/bio3d/issues
We are always interested in adding additional functionality to Bio3D. If you have ideas, suggestions or code that you would like to distribute as part of this package, please contact us (see below). You are also encouraged to contribute your code or issues directly to this repository for incorporation into the development version of the package. For details on how to do this please see the developer wiki.