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AlphaFold

  • Description

    an implementation of the inference pipeline of AlphaFold using a completely new model that was entered in CASP14.

  • Usage

    To list all executables provided by AlphaFold, run: $ sbgrid-list alphafold Copy to clipboard

  • Usage Notes

    AlphaFold requires a set of parameters and genetic databases that must be downloaded separately. See https://github.com/deepmind/alphafold#genetic-databases for more information.

    AlphaFold version 2 and version 3 have different parameters and databases and thus require different procedures.

    Please see our examples:

    SBGrid AlphaFold2 Example

    SBGrid AlphaFold3 Example

    Note that while the AlphaFold code is licensed under the open source Apache 2.0 License, the AlphaFold parameters are made available for non-commercial use only under the terms of the CC BY-NC 4.0 license. Please see the Disclaimer at https://github.com/deepmind/alphafold#license-and-disclaimer.

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install alphafold Copy to clipboard Available operating systems: Linux 64

  • Primary Citation*

    J. Jumper, R. Evans, A. Pritzel, T. Green, M. Figurnov, O. Ronneberger, K. Tunyasuvunakool, R. Bates, A. Žídek, A. Potapenko, A. Bridgland, C. Meyer, S. A. A. Kohl, A. J. Ballard, A. Cowie, B. Romera-Paredes, S. Nikolov, R. Jain, J. Adler, T. Back, S. Petersen, D. Reiman, E. Clancy, M. Zielinski, M. Steinegger, M. Pacholska, T. Berghammer, S. Bodenstein, D. Silver, O. Vinyals, A. W. Senior, K. Kavukcuoglu, P. Kohli, and D. Hassabis. 2021. Highly accurate protein structure prediction with AlphaFold. Nature.


    • *Full citation information available through

  • Webinars

    AlphaFold protein structures & ChimeraX cryoEM modeling

    Presenter: Tom Goddard, UCSF Resource for Biocomputing, Visualization, and Informatics - Topic: Using AlphaFold protein structures in ChimeraX for cryoEM modeling

    Linked to presented materials: https://www.rbvi.ucsf.edu/chimerax/data/sbgrid-mar2022/alphafold_pae.html

    Learn more on the ChimeraX website:
    https://www.rbvi.ucsf.edu/chimerax/data/alphafold-nov2021/af_sbgrid.html

    This talk was presented as part of the SBGrid Spring Mini-series - Cryo-electron microscopy of membrane proteins: from sample to structure. See the full series lineup at https://sbgrid.org/webinars/

    Organized by
    Prof. Jamaine Davis, Meharry Medical College
    Prof. Piotr Sliz, Harvard Medical School
    Prof. Patrick Sexton, ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash University

    Recorded on March 29, 2022

    Using AlphaFold protein structures in ChimeraX for cryoEM modeling

    Topic: Using AlphaFold protein structures in ChimeraX for cryoEM modeling

    Presenter: Tom Goddard, UCSF Resource for Biocomputing, Visualization, and Informatics

    Q&A session also includes Shaun Rawson, who presented during this session on "Effective on-the-fly and downstream processing of CryoEM data." See https://youtu.be/ra2sVFEPtN8

    Learn more on the ChimeraX website:
    https://www.rbvi.ucsf.edu/chimerax/data/alphafold-nov2021/af_sbgrid.html

    This talk was presented as part of the SBGrid Australasian III Mini-series - CryoEM: from Sample to Structure and should appeal to both novice and expert structural biologists.
    See the full mini-series lineup at https://sbgrid.org/news/sbgrid-university-otago-webinar-series.

  • Keywords

    Machine Learning, Protein-Protein Interaction Prediction, Protein Structure Analysis

  • Default Versions

    Linux 64:  3.0.1 (6.3 GB)

  • Other Versions

      Linux 64:

      2.1.2 (9.0 GB) , 2.2.0 (9.8 GB) , 2.2.2 (3.8 GB) , 2.2.3 (4.3 GB) , 2.2.4 (3.9 GB) , 2.3.0 (4.0 GB) , 2.3.1 (4.0 GB) , 2.3.2 (4.0 GB) , 2.3.2_20241024 (5.3 GB) , 3.0.0 (6.3 GB) , 3.0.0_20241202_aa724ca (6.3 GB)

  • Developers

    Tom Ward, Augustin Zidek, Saran Tunyasuvunakool, John Jumper, Demis Hassabis

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