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Alphafold

AlphaFold is an artificial intelligence program developed by DeepMind, a subsidiary of Alphabet, which performs predictions of protein structure.

Available modules

Alphafold2 is available as modules on Midway3 that you can check via module avail alphafold.

module avail alphafold
---------------------- /software/modulefiles----------------------------------
alphafold/2.0.0(default)  alphafold/2.2.0  alphafold/2.3.2

The AlphaFold source code and running scripts (e.g. run_alphafold.py) can be found at the Alphafold GitHub.

The training data sets for different versions of Alphafold are accessible under /software/alphafold-data/, /software/alphafold-data-2.2/ and /software/alphafold-data-2.3/.

Example job script

Typically, Alphafold2 uses OpenMM, a GPU-accelerated molecular simulation package, to relax the candidate protein. OpenMM requires the CUDA toolkit to run on a GPU node.

If you want to run on a CPU-only node without the relaxation run for the candidate protein, you can run the python script run_alphafold.py with --use_gpu_relax=false.

The following example job script illustrates how to use the alphafold/2.3.2 module on a GPU node with 2 GPUs and up to 16 CPU cores for multithreading on Midway3.

#!/bin/bash
#SBATCH --job-name=alphafold2
#SBATCH --account=[your-accountname]
#SBATCH --partition=gpu
#SBATCH --nodes=1
#SBATCH --time=04:00:00
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=16
#SBATCH --gres=gpu:2
#SBATCH --constraint=v100
#SBATCH --mem=64G

module load alphafold/2.3.2 cuda/11.3

cd $SLURM_SUBMIT_DIR

echo "GPUs available: GPU ID $CUDA_VISIBLE_DEVICES"
echo "CPU cores: $SLURM_CPUS_PER_TASK"

DOWNLOAD_DATA_DIR=/software/alphafold-data-2.3

python run_alphafold.py  \
  --data_dir=$DOWNLOAD_DATA_DIR  \
  --uniref90_database_path=$DOWNLOAD_DATA_DIR/uniref90/uniref90.fasta  \
  --mgnify_database_path=$DOWNLOAD_DATA_DIR/mgnify/mgy_clusters_2022_05.fa  \
  --bfd_database_path=$DOWNLOAD_DATA_DIR/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt  \
  --uniref30_database_path=$DOWNLOAD_DATA_DIR/uniref30/UniRef30_2021_03 \
  --pdb70_database_path=$DOWNLOAD_DATA_DIR/pdb70/pdb70  \
  --template_mmcif_dir=$DOWNLOAD_DATA_DIR/pdb_mmcif/mmcif_files  \
  --obsolete_pdbs_path=$DOWNLOAD_DATA_DIR/pdb_mmcif/obsolete.dat \
  --model_preset=monomer \
  --max_template_date=2022-1-1 \
  --db_preset=full_dbs \
  --use_gpu_relax=true \
  --output_dir=out_alphafold_2.1.1_multi-monomer \
  --fasta_paths=T1083.fasta,T1084.fasta