From 3d5441b22fb2b8e9c977016a92be8d724950eb3f Mon Sep 17 00:00:00 2001
From: Jan Siwiec <jan.siwiec@vsb.cz>
Date: Mon, 10 Jul 2023 11:46:47 +0200
Subject: [PATCH] Alphafold
---
.../software/machine-learning/alphafold.md | 27 +++++++++++++++++++
mkdocs.yml | 1 +
2 files changed, 28 insertions(+)
create mode 100644 docs.it4i/software/machine-learning/alphafold.md
diff --git a/docs.it4i/software/machine-learning/alphafold.md b/docs.it4i/software/machine-learning/alphafold.md
new file mode 100644
index 000000000..e51917dd1
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@@ -0,0 +1,27 @@
+# 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
diff --git a/mkdocs.yml b/mkdocs.yml
index f93381ec5..3bdf9f2e8 100644
--- a/mkdocs.yml
+++ b/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
--
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