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Software: Alphafold

Description

Alphafold is a protein structure prediction tool developed by DeepMind (Google). It uses a novel machine learning approach to predict 3D protein structures from primary sequences alone.

Available Versions

Unspecified: 2.1.1 2.2.0 2.2.3 2.3.0 2.3.1

The source code is available on Github. It has been deployed in all RCAC clusters, supporting both CPU and GPU.

It also relies on a huge database. The full database ( 2.2TB) has been downloaded and setup for users.

Protein struction prediction by alphafold is performed in the following steps:

  • Search the amino acid sequence in uniref90 database by jackhmmer (using CPU)
  • Search the amino acid sequence in mgnify database by jackhmmer (using CPU)
  • Search the amino acid sequence in pdb70 database (for monomers) or pdb_seqres database (for multimers) by hhsearch (using CPU)
  • Search the amino acid sequence in bfd database and uniclust30 (updated to uniref30 since v2.3.0) database by hhblits (using CPU)
  • Search structure templates in pdb_mmcif database (using CPU)
  • Search the amino acid sequence in uniprot database (for multimers) by jackhmmer (using CPU)
  • Predict 3D structure by machine learning (using CPU or GPU)
  • Structure optimisation with OpenMM (using CPU or GPU)

Commands

run_alphafold.sh

Module

You can load the modules by:

module load biocontainers
module load alphafold

Usage

The usage of Alphafold on our cluster is very straightford, users can create a flagfile containing the database path information:

run_alphafold.sh --flagfile=full_db.ff --fasta_paths=XX --output_dir=XX ...

Users can check its detailed user guide in its Github.

full_db.ff

Example contents of full_db.ff:

--db_preset=full_dbs
--bfd_database_path=/depot/itap/datasets/alphafold/db/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
--data_dir=/depot/itap/datasets/alphafold/db/
--uniref90_database_path=/depot/itap/datasets/alphafold/db/uniref90/uniref90.fasta
--mgnify_database_path=/depot/itap/datasets/alphafold/db/mgnify/mgy_clusters_2018_12.fa
--uniclust30_database_path=/depot/itap/datasets/alphafold/db/uniclust30/uniclust30_2018_08/uniclust30_2018_08
--pdb70_database_path=/depot/itap/datasets/alphafold/db/pdb70/pdb70
--template_mmcif_dir=/depot/itap/datasets/alphafold/db/pdb_mmcif/mmcif_files
--max_template_date=2022-01-29
--obsolete_pdbs_path=/depot/itap/datasets/alphafold/db/pdb_mmcif/obsolete.dat
--hhblits_binary_path=/usr/bin/hhblits
--hhsearch_binary_path=/usr/bin/hhsearch
--jackhmmer_binary_path=/usr/bin/jackhmmer
--kalign_binary_path=/usr/bin/kalign

Since Version v2.2.0, the AlphaFold-Multimer model parameters has been updated. The updated full database is stored in depot/itap/datasets/alphafold/db_20221014. For ACCESS Anvil, the database is stored in /anvil/datasets/alphafold/db_20221014. Users need to update the flagfile using the updated database:

run_alphafold.sh --flagfile=full_db_20221014.ff --fasta_paths=XX --output_dir=XX ...

full_db_20221014.ff (for alphafold v2)

Example contents of full_db_20221014.ff (For ACCESS Anvil, please change depot/itap to anvil):

--db_preset=full_dbs
--bfd_database_path=/depot/itap/datasets/alphafold/db_20221014/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
--data_dir=/depot/itap/datasets/alphafold/db_20221014/
--uniref90_database_path=/depot/itap/datasets/alphafold/db_20221014/uniref90/uniref90.fasta
--mgnify_database_path=/depot/itap/datasets/alphafold/db_20221014/mgnify/mgy_clusters_2018_12.fa
--uniclust30_database_path=/depot/itap/datasets/alphafold/db_20221014/uniclust30/uniclust30_2018_08/uniclust30_2018_08
--pdb_seqres_database_path=/depot/itap/datasets/alphafold/db_20221014/pdb_seqres/pdb_seqres.txt
--uniprot_database_path=/depot/itap/datasets/alphafold/db_20221014/uniprot/uniprot.fasta
--template_mmcif_dir=/depot/itap/datasets/alphafold/db_20221014/pdb_mmcif/mmcif_files
--obsolete_pdbs_path=/depot/itap/datasets/alphafold/db_20221014/pdb_mmcif/obsolete.dat
--hhblits_binary_path=/usr/bin/hhblits
--hhsearch_binary_path=/usr/bin/hhsearch
--jackhmmer_binary_path=/usr/bin/jackhmmer
--kalign_binary_path=/usr/bin/kalign

Since Version v2.3.0, the AlphaFold-Multimer model parameters has been updated. The updated full database is stored in depot/itap/datasets/alphafold/db_20230311. For ACCESS Anvil, the database is stored in /anvil/datasets/alphafold/db_20230311. Users need to update the flagfile using the updated database:

run_alphafold.sh --flagfile=full_db_20230311.ff --fasta_paths=XX --output_dir=XX ...

Since Version v2.3.0, uniclust30_database_path has been changed to uniref30_database_path.

full_db_20230311.ff (for alphafold v3)

Example contents of full_db_20230311.ff for monomer (For ACCESS Anvil, please change depot/itap to anvil):

--db_preset=full_dbs
--bfd_database_path=/depot/itap/datasets/alphafold/db_20230311/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
--data_dir=/depot/itap/datasets/alphafold/db_20230311/
--uniref90_database_path=/depot/itap/datasets/alphafold/db_20230311/uniref90/uniref90.fasta
--mgnify_database_path=/depot/itap/datasets/alphafold/db_20230311/mgnify/mgy_clusters_2022_05.fa
--uniref30_database_path=/depot/itap/datasets/alphafold/db_20230311/uniref30/UniRef30_2021_03
--pdb70_database_path=/depot/itap/datasets/alphafold/db_20230311/pdb70/pdb70
--template_mmcif_dir=/depot/itap/datasets/alphafold/db_20230311/pdb_mmcif/mmcif_files
--obsolete_pdbs_path=/depot/itap/datasets/alphafold/db_20230311/pdb_mmcif/obsolete.dat
--hhblits_binary_path=/usr/bin/hhblits
--hhsearch_binary_path=/usr/bin/hhsearch
--jackhmmer_binary_path=/usr/bin/jackhmmer
--kalign_binary_path=/usr/bin/kalign

Example contents of full_db_20230311.ff for multimer (For ACCESS Anvil, please change depot/itap to anvil):

--db_preset=full_dbs
--bfd_database_path=/depot/itap/datasets/alphafold/db_20230311/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
--data_dir=/depot/itap/datasets/alphafold/db_20230311/
--uniref90_database_path=/depot/itap/datasets/alphafold/db_20230311/uniref90/uniref90.fasta
--mgnify_database_path=/depot/itap/datasets/alphafold/db_20230311/mgnify/mgy_clusters_2022_05.fa
--uniref30_database_path=/depot/itap/datasets/alphafold/db_20230311/uniref30/UniRef30_2021_03
--pdb_seqres_database_path=/depot/itap/datasets/alphafold/db_20230311/pdb_seqres/pdb_seqres.txt
--uniprot_database_path=/depot/itap/datasets/alphafold/db_20230311/uniprot/uniprot.fasta
--template_mmcif_dir=/depot/itap/datasets/alphafold/db_20230311/pdb_mmcif/mmcif_files
--obsolete_pdbs_path=/depot/itap/datasets/alphafold/db_20230311/pdb_mmcif/obsolete.dat
--hhblits_binary_path=/usr/bin/hhblits
--hhsearch_binary_path=/usr/bin/hhsearch
--jackhmmer_binary_path=/usr/bin/jackhmmer
--kalign_binary_path=/usr/bin/kalign

Example job using CPU

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

Notice that since version 2.2.0, the parameter --use_gpu_relax=False is required.

To run alphafold using CPU:

#!/bin/bash
#SBATCH -A myallocation	# Allocation name 
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=alphafold
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers alphafold/2.3.1

run_alphafold.sh --flagfile=full_db_20230311.ff  \
    --fasta_paths=sample.fasta --max_template_date=2022-02-01 \
    --output_dir=af2_full_out --model_preset=monomer \
    --use_gpu_relax=False

Example job using GPU

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

Notice that since version 2.2.0, the parameter --use_gpu_relax=True is required.

To run alphafold using GPU:

#!/bin/bash
#SBATCH -A myallocation	# Allocation name 
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 11
#SBATCH --gres=gpu:1
#SBATCH --job-name=alphafold
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers alphafold/2.3.1

run_alphafold.sh --flagfile=full_db_20230311.ff \
    --fasta_paths=sample.fasta --max_template_date=2022-02-01 \
    --output_dir=af2_full_out --model_preset=monomer \
    --use_gpu_relax=True