AlphaFold 2.2.2-foss-2021a-CUDA-11.3.1

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

Accessing AlphaFold 2.2.2-foss-2021a-CUDA-11.3.1

To load the module for AlphaFold 2.2.2-foss-2021a-CUDA-11.3.1 please use this command on Baskerville:

module load bask-apps/live
module load AlphaFold/2.2.2-foss-2021a-CUDA-11.3.1

Bask Apps Env

live

AlphaFold Databases

The AlphaFold databases, include both the full and reduced versions, are available in ${BASK_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 $ALPHAFOLD_DATA_DIR environment variable for it to pick up all the data provided in that location. So, adding export ALPHAFOLD_DATA_DIR=${BASK_APPS_DATA}/AlphaFold/20220825 to your jobscript will be sufficient for the centrally downloaded databases to be detected.

Extensions

  • chex 0.1.3
  • contextlib2 21.6.0
  • dm-haiku-0.0.6
  • dm-tree-0.1.7
  • docker 5.0.3
  • immutabledict 2.2.1
  • jmp 0.0.2
  • ml_collections 0.1.1
  • PDBFixer 1.7
  • tabulate 0.8.10
  • toolz 0.11.2
  • websocket-client-1.3.3

More Information

For more information visit the AlphaFold website.

Dependencies

This version of AlphaFold has a direct dependency on: Biopython/1.79-foss-2021a CUDA/11.3.1 cuDNN/8.2.1.32-CUDA-11.3.1 foss/2021a HH-suite/3.3.0-gompi-2021a HMMER/3.3.2-gompi-2021a jax/0.3.9-foss-2021a-CUDA-11.3.1 Kalign/3.3.1-GCCcore-10.3.0 NCCL/2.10.3-GCCcore-10.3.0-CUDA-11.3.1 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-CUDA-11.3.1 UCX-CUDA/1.10.0-GCCcore-10.3.0-CUDA-11.3.1

Last modified on 22nd August 2022