Bio3D-web is an online application for the interactive exploration and analysis of biomolecular structure data. This app provides an online interface to a subset of Bio3D package functionality including:
- The identification of related protein structure sets to user specified thresholds of similarity;
- Their multiple alignment and structure superposition;
- Sequence and structure conservation analysis;
- Inter-conformer relationship mapping with principal component analysis, and
- Comparison of predicted internal dynamics via ensemble normal mode analysis.
This integrated functionality provides a complete workflow for beginning the investigation of sequence-structure-dynamic relationships.
Bio3D-web can be accessed and run from our online server using any major web browser.
You can also install Bio3D-web locally on any computer running R by following the instructions below.
The simplest method is to install directly from bitbucket using the R function
install_bitbucket() from the devtools package.
> library(devtools) > install_bitbucket("Grantlab/bio3d", ref = "feature_shiny", subdir = "ver_devel/bio3d/")
Download and install manually
Build and install from source
Once downloaded and uncompressed, enter the main directory of Bio3D. Open a terminal session:
$ cd ver_devel
Type following commands to build and install:
$ R CMD build bio3d $ R CMD INSTALL bio3d_XXX.tar.gz
where XXX is the version number of Bio3D you have built.
We will now install R dependencies for Bio3D-web 'pca-app'. Open a terminal session and enter the main directory of Bio3D:
$ cd shiny_devel/pca-app
Open a R session, followed by:
You are now ready to run Bio3D-web locally. To launch:
$ R -e "shiny::runApp()"
Optional: Please see the README under
shiny_devel/pca-app on how to download all PDB sequences in FASTA format and set up a local MySQL database for speed-up. The location of PDB sequences FASTA file and the details regarding MySQL setup should be updated in
For any issues with the pca-app, you are welcome to:
- Submit suggestions and bug-reports at: https://bitbucket.org/Grantlab/bio3d/issues
- Compose a friendly e-mail to: firstname.lastname@example.org or email@example.com