Alphafold

docs.it4i/software/machine-learning/alphafold.md

+# AlphaFold
+
+[AlphaFold][1] is an AI program designed as a deep learning system
+developed by DeepMind, a subsidiary of Alphabet,
+which performs predictions of protein structure.
+
+## Installed Versions
+
+AlphaFold is available on the Karolina cluster.
+For the current list of installed versions, use:
+
+```console
+ml av alphafold
+```
+
+## Loading Databases
+
+AlphaFold needs multiple genetic databases to run.
+These can be downloaded using AlphaFold scripts located in the `apps/all/AlphaFold/2.1.2-fosscuda-2020b-TensorFlow-2.5.0/scripts` directory.
+This step requires the `aria2c` program available as the `aria2/1.35.0-GCCcore-10.3.0` module.
+
+Once downloaded, you must specify the path to the directory on `/scratch` containing the databases.
+
+For more information, see the [AlphaFold documentation][2].
+
+[1]: https://www.deepmind.com/research/highlighted-research/alphafold
+[2]: https://github.com/deepmind/alphafold#genetic-databases

mkdocs.yml

@@ -234,6 +234,7 @@ nav:
       - NetKet: software/machine-learning/netket.md
       - TensorFlow: software/machine-learning/tensorflow.md
       - Deep Learning:
+          - AlphaFold: software/machine-learning/alphafold.md
           - DeepDock: software/machine-learning/deepdock.md
     - MPI:
       - Introduction: software/mpi/mpi.md