AlphaFold3

AlphaFold3

AlphaFold3 is a cutting-edge AI system developed by DeepMind for predicting protein structures with high accuracy. Building on its predecessors, AlphaFold3 integrates additional molecular modeling capabilities, making it a powerful tool for structural biology research.

This guide provides step-by-step instructions on setting up and running AlphaFold3 on UBELIX using Slurm.

Directory Structure Setup

Before running AlphaFold3, set up the necessary directory structure.

1. Choose a suitable location for AlphaFold3. For example:

   bash

   export AF3_ROOT=~/alphafold3/

2. Create the required directories:

   bash

   mkdir -p $AF3_ROOT
   mkdir -p $AF3_ROOT/input             # Store input JSON files
   mkdir -p $AF3_ROOT/output            # Store generated structure outputs
   mkdir -p $AF3_ROOT/model_parameters  # Store downloaded model parameters
   mkdir -p $AF3_ROOT/databases         # Store public databases

Cloning the AlphaFold3 Repository

Clone the official AlphaFold3 source code from GitHub:

bash

cd $AF3_ROOT
git clone https://github.com/google-deepmind/alphafold3.git src

Creating the Slurm Submission Script

Create a Slurm submission script (e.g., run_alphafold3.sh) for running AlphaFold3 on a GPU node.

1. Navigate to the project directory:

   bash

   cd $AF3_ROOT

2. Create run_alphafold3.sh and add the following content:

   bash

   #!/bin/bash
   #SBATCH --job-name="alphafold3_job"
   #SBATCH --time=01:00:00
   #SBATCH --partition=gpu
   #SBATCH --gres=gpu:rtx4090:1
   #SBATCH --cpus-per-task=16
   #SBATCH --mem-per-cpu=5760M
   
   module load CUDA/12.6
   
   singularity exec \
        --nv \
        --bind $PWD/input:/root/af_input \
        --bind $PWD/output:/root/af_output \
        --bind $PWD/model_parameters:/root/models \
        --bind $PWD/databases:/root/public_databases \
        /storage/software/singularity/containers/alphafold3.sif \
        python src/run_alphafold.py \
        --json_path=/root/af_input/fold_input.json \
        --model_dir=/root/models \
        --db_dir=/root/public_databases \
        --output_dir=/root/af_output

3. Save and close the file

Downloading Public Databases

AlphaFold3 requires publicly available databases for structure prediction.

Danger: Very large databases

The AlphaFold3 databases are nearly 650GB in size. To avoid redundant downloads and conserve storage, it is recommended that a single copy be maintained in a shared workspace for the entire lab. Check with colleagues and supervisors if a copy of the databases is already accessible to you!

Link existing databases

If the public databases are already available, simply create a symbolic link to their location:

bash

cd $AF3_ROOT
ln -s /path/to/workspace/databases databases

Install databases to shared workspace

1. Navigate to the shared workspace to store the dabases, e.g.:

   bash

   cd /path/to/workspace/alphafold3/databases

2. Download the database fetch script:

   bash

   wget https://raw.githubusercontent.com/google-deepmind/alphafold3/refs/heads/main/fetch_databases.sh

3. Make the script executable and run it:

   bash

   chmod u+x fetch_databases.sh
   ./fetch_databases.sh databases

4. Continue with lining existing databases

bash

cd $AF3_ROOT
ln -s /path/to/workspace/databases databases

**Install databases to user home **

1. Navigate to the AlphaFold3 project directory:

   bash

   cd $AF3_ROOT

2. Download the database fetch script:

   bash

   wget https://raw.githubusercontent.com/google-deepmind/alphafold3/refs/heads/main/fetch_databases.sh

3. Make the script executable and run it:

   bash

   chmod u+x fetch_databases.sh
   ./fetch_databases.sh databases

Downloading Model Parameters

AlphaFold3 model parameters need to be downloaded separately. To request access to the model parameters, please complete this form. Access will be granted at Google DeepMind’s sole discretion. You may only use AlphaFold 3 model parameters if received directly from Google. Use is subject to these terms of use.

Ensure they are stored in the model_parameters directory:

bash

cd $AF3_ROOT/model_parameters
# Download and extract model parameters following official AlphaFold3 instructions.

Preparing Input File

AlphaFold3 requires a JSON input file containing sequence and configuration details. Create an input file at input/fold_input.json:

Example:

json

{
  "name": "2PV7",
  "sequences": [
    {
      "protein": {
        "id": ["A", "B"],
        "sequence": "GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG"
      }
    }
  ],
  "modelSeeds": [1],
  "dialect": "alphafold3",
  "version": 1
}

Submitting the Job

Once everything is set up, submit the job to Slurm:

bash

sbatch run_alphafold3.sh

Output Location

Once the job is complete, the predicted structures will be available in:

$AF3_ROOT/output/