AlphaFold 2.1.1-foss-2021a
Unsupported: Use of this version of AlphaFold is not supported. More information on our Applications Support and Retention Policy.
There is a newer version of AlphaFold
AlphaFold can predict protein structures with atomic accuracy even where no similar structure is knownAccessing AlphaFold 2.1.1-foss-2021a
To load the module for AlphaFold 2.1.1-foss-2021a please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):
module load bear-apps-unsupported/handbuilt/2019
module load AlphaFold/2.1.1-foss-2021a
There is a GPU enabled version of this module: AlphaFold 2.1.1-foss-2021a-CUDA-11.3.1
BEAR Apps Version
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 0.0.8
- contextlib2 21.6.0
- dm-haiku-0.0.4
- dm-tree-0.1.6
- docker 5.0.0
- immutabledict 2.1.0
- ml_collections 0.1.0
- PDBFixer 1.7
- tabulate 0.8.9
- toolz 0.11.1
- websocket-client-1.2.1
More Information
For more information visit the AlphaFold website.
Dependencies
This version of AlphaFold has a direct dependency on: Biopython/1.79-foss-2021a foss/2021a HH-suite/3.3.0-gompi-2021a HMMER/3.3.2-gompi-2021a jax/0.2.24-foss-2021a Kalign/3.3.1-GCCcore-10.3.0 Python/3.9.5-GCCcore-10.3.0 PyYAML/5.4.1-GCCcore-10.3.0 SciPy-bundle/2021.05-foss-2021a TensorFlow/2.6.0-foss-2021a
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.
Version | BEAR Apps Version |
---|---|
2.3.1-foss-2022a | 2022a |
2.3.1-foss-2022a-CUDA-11.7.0 | 2022a |
2.2.2-foss-2021a-CUDA-11.3.1 | 2021a |
2.1.1-foss-2021a-CUDA-11.3.1 | 2021a |
Last modified on 29th November 2021