AlphaFold 2.3.1-foss-2022a

AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known

Accessing AlphaFold 2.3.1-foss-2022a

To load the module for AlphaFold 2.3.1-foss-2022a please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load bear-apps/2022a
module load AlphaFold/2.3.1-foss-2022a

There is a GPU enabled version of this module: AlphaFold 2.3.1-foss-2022a-CUDA-11.7.0

BEAR Apps Version

2022a

Architectures

EL8-cascadelakeEL8-icelake

The listed architectures consist of two part: OS-CPU. The OS used is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.

AlphaFold Databases

The AlphaFold databases, include both the full and reduced versions, are available in ${BB_APPS_DATA}/AlphaFold. Inside that folder you will find folder(s) dated by download date. Each dated folder contains all of the databases that can be downloaded with the download_all_data.sh script and was downloaded on the date as indicated by the folder name.

Running AlphaFold

For convenience a symbolic link named alphafold points to the run_alphafold.py script. So, once the AlphaFold module is loaded, you can just use alphafold instead of run_alphafold.py or python run_alphafold.py.

The run_alphafold.py script has been modified so that it is sufficient to define the $ALPHAFOLD_DATA_DIR environment variable for it to pick up all the data provided in that location. So, adding export ALPHAFOLD_DATA_DIR=${BB_APPS_DATA}/AlphaFold/20211118 to your jobscript will be sufficient for the centrally downloaded databases to be detected.

Extensions

  • chex 0.1.6
  • contextlib2 21.6.0
  • dm-haiku-0.0.9
  • dm-tree-0.1.8
  • docker 6.0.1
  • immutabledict 2.2.3
  • jmp 0.0.4
  • ml_collections 0.1.1
  • PDBFixer 1.8.1
  • tabulate 0.9.0
  • toolz 0.12.0
  • websocket-client-1.5.1

More Information

For more information visit the AlphaFold website.

Dependencies

This version of AlphaFold has a direct dependency on: Biopython/1.79-foss-2022a foss/2022a HH-suite/3.3.0-gompi-2022a HMMER/3.3.2-gompi-2022a jax/0.3.23-foss-2022a Kalign/3.3.5-GCCcore-11.3.0 OpenMM/7.7.0-foss-2022a Python/3.10.4-GCCcore-11.3.0 PyYAML/6.0-GCCcore-11.3.0 SciPy-bundle/2022.05-foss-2022a TensorFlow/2.11.0-foss-2022a

Other Versions

These versions of AlphaFold are available on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 4th April 2023