Alphafold

Overview

• DeepMind: AlphaFold: can accurately predict 3D models of protein structures and has the potential to accelerate research in every field of biology.

Documentation

• AlphaFold Protein Structure Database: Developed by DeepMind and EMBL-EBI

• AlphaFold Colab: “This Colab notebook allows you to easily predict the structure of a protein using a slightly simplified version of AlphaFold v2.1.0.“

• General Articles:

  • Deepmind: AlphaFold

  • Putting the power of AlphaFold into the world’s hands.

• ARCC are NOT domain experts on the science behind using Alphafold. We can best effort support on errors you come across, but not the use of the flags and databases used by Alphafold.

  • Please share any feedback you have, and we will develop this page for the wider community.

Using

Use the module name alphafold to discover versions available and to load the application.

Loading the particular alphafold module version will appropriate set the following environment variables: ALPHADB and ALPHABIN and set the associated singularity module version.

Running Alphafold

Alphafold has been built via a docker image, but has been converted to a Singularity image, so must be run using Singularity.

Flag Help

As versions of alphafold update, available options will change. On loading the alphafold module, a full list of flags can be found by running:

Data Files and Examples