Supported Applications

Description

an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.

Usage

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

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.

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  *Full citation information available through

• AppCiter

Webinars

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

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.