AlphaFold 2

AlphaFold is an AI system developed by the Google DeepMind project to predict the 3D structure of a protein from its amino acid sequence. AlphaFold needs multiple datasets to run, the combined size of which is around 2.62 TB. It takes a long time to download them. We save you that effort by locating these datasets at /contrib/datasets/alphafold.

We also host containers at /contrib/singularity/alphafold that you can use with the provided datasets to predict protein structures with AlphaFold. You can access the container by loading the alphafold module from an interactive session or a batch submission script. When you load the alphafold module, it defines the following additional environment variables that you can use to easily access the container and the datasets:

ALPHAFOLD_DIR which points to /contrib/singularity/alphafold
ALPHAFOLD_DATADIR which points to /contrib/datasets/alphafold

The following batch submission script shows how you can use the container with the provided datasets.

#!/bin/bash
#SBATCH --job-name=alphafold-run
#SBATCH --time=04:00:00
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --ntasks-per-node=1
#SBATCH --partition=standard
#SBATCH --account=<pi-account>

# Uncomment the following two lines to make predictions on proteins that would be too long to fit into GPU memory.
# export APPTAINERENV_TF_FORCE_UNIFIED_MEMORY=1  
# export APPTAINERENV_XLA_PYTHON_CLIENT_MEM_FRACTION=4.0

module load alphafold

apptainer run \
          -B .:/etc \
          -B $ALPHAFOLD_DATADIR:/data \
          --pwd /app/alphafold $ALPHAFOLD_DIR/alphafold-2.3.0.sif \
          --data_dir=/data  \
          --nv \
          --use_gpu_relax \
          --uniref90_database_path=/data/uniref90/uniref90.fasta  \
          --uniref30_database_path=/data/uniref30/UniRef30_2021_03 \
          --mgnify_database_path=/data/mgnify/mgy_clusters_2022_05.fa  \
          --bfd_database_path=/data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt  \
          --pdb70_database_path=/data/pdb70/pdb70  \
          --template_mmcif_dir=/data/pdb_mmcif/mmcif_files  \
          --obsolete_pdbs_path=/data/pdb_mmcif/obsolete.dat \
          --model_preset=monomer \
          --max_template_date=2023-08-02 \
          --db_preset=full_dbs \
          --output_dir=results \
          --fasta_paths=input.fasta

Browser not supported