diff --git a/docs.it4i/software/machine-learning/alphafold.md b/docs.it4i/software/machine-learning/alphafold.md new file mode 100644 index 0000000000000000000000000000000000000000..e51917dd13ff7149d5c59ad2f131ce7f36795a4b --- /dev/null +++ b/docs.it4i/software/machine-learning/alphafold.md @@ -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 f93381ec598be29e2167255851f4e6256018a69b..3bdf9f2e85a7d79a45df9148622d97bd3f1c859e 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