alphafold: AlphaFold Protein Structure Database and Software

Overview of package

Package:	alphafold
Description:	AlphaFold Protein Structure Database and Software
For more information:	https://alphafold.com
Categories:	SoftwareDevelopment NumericalMethods
License:	OpenSource (CC-BY 4.0)

General Usage

AlphaFold is an AI system that predicts the 3D structure of a protein from its amino acid sequence.

This module will set various environmental variables and activate a conda environment in which you can run the various AlphaFold python scripts.

Included is an abridged version of the AlphaFold database. Please contact HPC support staff at hpcc-help@umd.edu if there are additional portions of the database needed. Installed databases include: * bfd * mgnify * pdb70 * pdb_seqres * small_bfd * uniclust30 * uniprot * uniref30 * uniref90

The following environmental variables which might be useful in your scripts are defined: * ALPHAFOLD_ROOT: points to root of the AlphaFold software * ALPHAFOLD_DATABASE_DIR: points to the top of AlphaFold DB * ALPHAFOLD_DIR: points to root of the AlphaFold software * ALPHAFOLD_CONDA_ENV: points to conda environment for AlphaFold

Available versions by cluster

This section lists the available versions of the package alphafoldon the UMD HPC clusters.

Versions available on the Zaratan cluster

Version	Module tags	CPU(s) optimized for	GPU ready?
2.3.2	2.3.2	x86_64	Yes
2.3.2-icelake	2.3.2-icelake	icelake	Yes