alphafold

Summary

Software Description

Alphafold is an AI-based protein structure inference pipeline developed by DeepMind, which can predict a protein’s 3D structure from its amino acid sequence.

General Linux

You can load alphafold for use in a Linux environment via:

module load alphafold

Running alphafold at MSI is a little different than what is indicated in DeepMind’s original documentation. Since we are using a non-docker implementation based on https://github.com/kalininalab/alphafold_non_docker , we need to adapt our workflow accordingly. A workflow might look like:

module load alphafold

# We need a symlink to this directory wherever we are running alphafold, since several reference files are
# supposed to be located in ./alphafold
cd project_dir
ln -s $alphafold_path alphafold 2>/dev/null || true

# Use a provided wrapper script to invoke the pipeline
run_alphafold.sh -o ./output_directory -m model_1 -f ./input/my_fasta.fasta -t 2020-05-14

Slurm Example

An example script for submission to the msigpu partition is provided below. Note that you will need to customize this script with your email (replacing sample_email@umn.edu), specific project directory (replacing project_dir), and input/output file locations (replacing ./output and ./input/my_fasta.fasta).

msigpu:

#!/bin/bash -l
#SBATCH --time=24:00:00
#SBATCH --ntasks=24
#SBATCH --mem=20g
#SBATCH --tmp=100g
#SBATCH -p msigpu
#SBATCH --gres=gpu:v100:2
#SBATCH --mail-type=ALL
#SBATCH --mail-user=sample_email@umn.edu

module load alphafold/2.0
cd project_dir
ln -s $alphafold_path alphafold  2>/dev/null || true
run_alphafold.sh -o ./output -m model_1 -f ./input/my_fasta.fasta -t 2020-05-14

msigpu multimer workflow:

#!/bin/bash -l
#SBATCH --time=24:00:00
#SBATCH --ntasks=24
#SBATCH --mem=20g
#SBATCH --tmp=100g
#SBATCH -p msigpu
#SBATCH --gres=gpu:v100:2
#SBATCH --mail-type=ALL
#SBATCH --mail-user=sample_email@umn.edu

module load alphafold/2.1.1-multimer
cd project_dir
ln -s $alphafold_path alphafold  2>/dev/null || true
run_alphafold.sh -o ./output -m multimer -f ./input/my_multimer_fasta.fasta -t 2021-11-01