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alphafold: AlphaFold Protein Structure Database and Software

Contents

  1. Overview of package
    1. General usage
  2. Availability of package by cluster

Overview of package

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

General usage information

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 of the package alphafold, by cluster

This section lists the available versions of the package alphafoldon the different clusters.

Available versions of alphafold on the Zaratab cluster

Available versions of alphafold on the Zaratab cluster
Version Module tags CPU(s) optimized for GPU ready?
2.3.2-icelake alphafold/2.3.2-icelake icelake Y
2.3.2 alphafold/2.3.2 x86_64 Y






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