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bio3d / How to install Bio3D-web locally on your own computer

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:

  1. The identification of related protein structure sets to user specified thresholds of similarity;
  2. Their multiple alignment and structure superposition;
  3. Sequence and structure conservation analysis;
  4. Inter-conformer relationship mapping with principal component analysis, and
  5. 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.

Use devtools

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

The source code is available in zip, gz and bz2 formats. Please visit Downloads and then Tags (for releases) or Branches (for development) versions of Bio3D.

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.

Check dependencies

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:

> source("dependencies.R")

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 config.r (under shiny_devel/pca-app).


For any issues with the pca-app, you are welcome to: