AlphaFold 2.3.1-foss-2022a
There is a newer install of AlphaFold
AlphaFold can predict protein structures with atomic accuracy even where no similar structure is knownAccessing 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 and BEAR Cloud 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
Architectures
EL8-cascadelake — EL8-icelake — EL8-sapphirerapids
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. We provide several database downloads from different dates in ${BB_APPS_DATA}/AlphaFold. Select one of these centrally downloaded databases to use and add the following to your jobscript (replacing YYYYMMDD with the relevant database date):
export ALPHAFOLD_DATA_DIR=${BB_APPS_DATA}/AlphaFold/YYYYMMDD
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 and BEAR Cloud VMs). These will be retained in accordance with our Applications Support and Retention Policy.
Last modified on 4th April 2023