AlphaFold

Software description

This open source code provides an implementation of the AlphaFold v2 system. It allows users to predict the 3-D structure of arbitrary proteins with unprecedented accuracy. AlphaFold v2 is a completely new model that was entered in the CASP14 assessment and published in Nature (Jumper et al. 2021). The package contains source code, trained weights, and an inference script.

If you want to use your own installation of AlphaFold, you can find the required data bases under /proj/common_datasets/AlphaFold

Homepage: github.com/deepmind/alphafold

Available Modules

v2.2.0-nsc1

Installation of AlphaFold v2.2.0 based on the official Docker from DeepMind.

Job script example - large database

#!/bin/bash

#SBATCH -A snic202X-Y-ZZ  # your allocation account
#SBATCH --gpus=1          # number of GPUs (don't change)
#SBATCH --nodes=1         # number of nodes (don't change)
#SBATCH --time=05:00:00   # time

module load AlphaFold/v2.2.0-nsc1

run_singularity_af --fasta_paths=$(pwd -P)/T1050.fasta \
    --output_dir=$(pwd -P) \
    --model_preset=monomer \
    --db_preset=full_dbs \
    --bfd_database_path=/data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
    --pdb70_database_path=/data/pdb70/pdb70 \
    --uniclust30_database_path=/data/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
    --max_template_date=2020-05-14 \
    --use_gpu_relax=True

Job script example - small database

#!/bin/bash

#SBATCH -A snic202X-Y-ZZ  # your allocation account
#SBATCH --gpus=1          # number of GPUs (don't change)
#SBATCH --nodes=1         # number of nodes (don't change)
#SBATCH --time=02:00:00   # time

module load AlphaFold/v2.2.0-nsc1

run_singularity_af --fasta_paths=$(pwd -P)/T1050.fasta \
    --output_dir=$(pwd -P) \
    --model_preset=monomer \
    --db_preset=reduced_dbs \
    --small_bfd_database_path=/data/small_bfd/bfd-first_non_consensus_sequences.fasta \
    --pdb70_database_path=/data/pdb70/pdb70 \
    --max_template_date=2020-05-14 \
    --use_gpu_relax=True

Load with:

[user@system ~]$ module load AlphaFold/v2.2.0-nsc1

3.0.1-hpc1

Load with:

[user@system ~]$ module load AlphaFold/3.0.1-hpc1

3.0.0-hpc1

Load with:

[user@system ~]$ module load AlphaFold/3.0.0-hpc1

2.3.2-hpc1

Load with:

[user@system ~]$ module load AlphaFold/2.3.2-hpc1

2.3.1-hpc1

Load with:

[user@system ~]$ module load AlphaFold/2.3.1-hpc1