AlphaFold¶

Description¶

This package provides a container that can be used to run AlphaFold 3.0. Due to licensing restrictions, it does not provide a complete installation. Individual researchers must obtain approval from Google to download the model parameters required by AlphFold 3.

Environment Modules¶

Run module spider alphafold3 to find out what environment modules are available for this application.

Environment Variables¶

HPC_ALPHAFOLD_IMG - container image
HPC_ALPHAFOLD_REF - reference directory

Additional Usage Information¶

Obtaining model parameters¶

Prior to running AlphaFold 3, individual researchers must obtain the model parameters. To request access to the AlphaFold 3 model parameters, please complete this form.

Genetic Databases¶

AlphaFold3 also requires a writable directory of genetic database files. The files can be found in /data/reference/alphafold/3.0.0 but will need to be copied or linked to a user writable directory.

Running AlphaFold¶

The following commands are adapted from the AlphaFold documentation:

ml alphafold3
export AF_WORKDIR = /blue/mygroup/username/alphafold

apptainer exec \
  --nv \
  --bind /data/reference/alphafold/3.0.0:/root/databases \
  $HPC_ALPHAFOLD_IMG \
  python run_alphafold.py \
  --json_path=$AF_WORKDIR/af_input/fold_input.json \
  --model_dir=$AF_WORKDIR/models \
  --db_dir=/root/databases \
  --output_dir=$AF_WORKDIR/af_output

Categories¶

protein, structure, machine_learning