# alphafold

## Summary

+ **Module Name:** alphafold
+ **Support Level:** Secondary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [https://github.com/deepmind/alphafold](https://github.com/deepmind/alphafold)

## 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