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AlphaFold

  • Description

    an implementation of the inference pipeline of AlphaFold v2.0 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.

    These parameters and databases can be downloaded with the included download script and the aria2c program, both of which are available in the SBGrid collection. Note that these databases are large in size (> 2Tb) and may require a significant amount of time to download.

    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.

    Please see https://sbgrid.org//wiki/examples/alphafold2 for more information about using alphafold in SBGrid and BioGrids.

  • 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.

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