AlphaFold

AlphaFold is an AI program designed as a deep learning system developed by DeepMind, a subsidiary of Alphabet, which performs predictions of protein structure.

Installed Versions

AlphaFold is available on the Karolina cluster. For the current list of installed versions, use:

ml av alphafold

Loading Databases

AlphaFold needs multiple genetic databases to run. These can be downloaded using AlphaFold scripts located in the apps/all/AlphaFold/2.1.2-fosscuda-2020b-TensorFlow-2.5.0/scripts directory. This step requires the aria2c program available as the aria2/1.35.0-GCCcore-10.3.0 module.

Once downloaded, you must specify the path to the directory on /scratch containing the databases.

For more information, see the AlphaFold documentation.