Alphafold 3 Usage on Sol

Access

AlphaFold 3 is available for all ASU users as an Apptainer container.

The AlphaFold 3 source code is licensed under the Creative Commons Attribution-Non-Commercial ShareAlike International License, Version 4.0 (CC-BY-NC-SA 4.0) (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at https://github.com/google-deepmind/alphafold3/blob/main/LICENSE .

Obtaining Model Parameters

The AlphaFold 3 model parameters are made available under the AlphaFold 3 Model Parameters Terms of Use (the "Terms"); you may not use these except in compliance with the Terms. You may obtain a copy of the Terms at https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md .

Due to the Terms of Use, ASU will no longer maintain the model parameters in a central location. Users must download them by following the instructions at: https://github.com/google-deepmind/alphafold3?tab=readme-ov-file#obtaining-model-parameters

Usage

Here is an example sbatch script to run Alphafold3.

#!/bin/bash

#SBATCH -N 1
#SBATCH -c 16
#SBATCH -p general
#SBATCH -q public
#SBATCH --time=0-01:00:00
#SBATCH -G a100:1
#SBATCH --mem=32G
#SBATCH -o slurm.%j.out # file to save job's STDOUT (%j = JobId)
#SBATCH -e slurm.%j.err # file to save job's STDERR (%j = JobId)
#SBATCH --mail-type=ALL # Send an e-mail when a job starts, stops, or fails
#SBATCH --mail-user="%u@asu.edu"
#SBATCH --export=NONE   # Purge the job-submitting shell environment"

module load cuda-12.6.1-gcc-12.1.0

#set the environment PATH
export PYTHONNOUSERSITE=True
export PARAMS=/scratch/$USER/alphafold3/paramaters    # edit this line
export USER_DIR=/scratch/$USER/alphafold3             # edit this line
export DB=/data/alphafold/alphafold3/db_20250131
export CONTAINER=/packages/apps/simg/alphafold-3.0.1.sif
export INPUT=input.json

apptainer exec \
     --nv \
     --bind $USER_DIR/af_input:/root/af_input \
     --bind $USER_DIR/af_output:/root/af_output \
     --bind $PARAMS:/root/models \
     --bind $DB:/root/public_databases \
     $CONTAINER \
     python /app/alphafold/run_alphafold.py \
     --json_path=/root/af_input/$INPUT \
     --model_dir=/root/models \
     --db_dir=/root/public_databases \
     --output_dir=/root/af_output

The following directories need to be created for input and output for alphafold. in this example we are using /scratch

/scratch/$USER/alphafold3
/scratch/$USER/alphafold3/af_input
/scratch/$USER/alphafold3/af_output
/scratch/$USER/alphafold3/params

Edit lines 20 and 21 for paths to user-specific directories, see above.

Input

Alphafold 3 docs on input JSON file - Input

here is a simple example of an input JSON

input.json

{
  "name": "test",
  "sequences": [
    {
      "protein": {
        "id": ["A", "B"],
        "sequence": "GSREGTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRRIARIQQIEKDILRIRQLLQSQATEAERSSQNKH"
      }
    }
  ],
  "modelSeeds": [1],
  "dialect": "alphafold3",
  "version": 1
}

Output

Alphafold 3 docs on output data - Output

Citing This Work

Any publication that discloses findings arising from using this source code, the model parameters or outputs produced by those should cite:

@article{Abramson2024,
  author  = {Abramson, Josh and Adler, Jonas and Dunger, Jack and Evans, Richard and Green, Tim and Pritzel, Alexander and Ronneberger, Olaf and Willmore, Lindsay and Ballard, Andrew J. and Bambrick, Joshua and Bodenstein, Sebastian W. and Evans, David A. and Hung, Chia-Chun and O’Neill, Michael and Reiman, David and Tunyasuvunakool, Kathryn and Wu, Zachary and Žemgulytė, Akvilė and Arvaniti, Eirini and Beattie, Charles and Bertolli, Ottavia and Bridgland, Alex and Cherepanov, Alexey and Congreve, Miles and Cowen-Rivers, Alexander I. and Cowie, Andrew and Figurnov, Michael and Fuchs, Fabian B. and Gladman, Hannah and Jain, Rishub and Khan, Yousuf A. and Low, Caroline M. R. and Perlin, Kuba and Potapenko, Anna and Savy, Pascal and Singh, Sukhdeep and Stecula, Adrian and Thillaisundaram, Ashok and Tong, Catherine and Yakneen, Sergei and Zhong, Ellen D. and Zielinski, Michal and Žídek, Augustin and Bapst, Victor and Kohli, Pushmeet and Jaderberg, Max and Hassabis, Demis and Jumper, John M.},
  journal = {Nature},
  title   = {Accurate structure prediction of biomolecular interactions with AlphaFold 3},
  year    = {2024},
  volume  = {630},
  number  = {8016},
  pages   = {493–-500},
  doi     = {10.1038/s41586-024-07487-w}
}

Research Computing