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Highly accurate protein structure prediction for the human proteome – nature.com

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Abstract

Protein structures can provide invaluable information, both for reasoning about biological processes and for enabling interventions such as structure-based drug development or targeted mutagenesis. After decades of effort, 17% of the total residues in human protein sequences are covered by an experimentally-determined structure1. Here we dramatically expand structural coverage by applying the state-of-the-art machine learning method, AlphaFold2, at scale to almost the entire human proteome (98.5% of human proteins). The resulting dataset covers 58% of residues with a confident prediction, of which a subset (36% of all residues) have very high confidence. We introduce several metrics developed by building on the AlphaFold model, and use them to interpret the dataset, identifying strong multi-domain predictions as well as regions likely to be disordered. Finally, we provide some case studies illustrating how high-quality predictions may be used to generate biological hypotheses. Importantly, we are making our predictions freely available to the community via a public database (hosted by the European Bioinformatics Institute at https://alphafold.ebi.ac.uk/). We anticipate that routine large-scale and high-accuracy structure prediction will become an important tool, allowing new questions to be addressed from a structural perspective.

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Author notes

  1. These authors contributed equally: John Jumper, Demis Hassabis

Affiliations

  1. DeepMind, London, UK

    Kathryn Tunyasuvunakool, Jonas Adler, Zachary Wu, Tim Green, Michal Zielinski, Augustin Žídek, Alex Bridgland, Andrew Cowie, Clemens Meyer, Agata Laydon, Richard Evans, Alexander Pritzel, Michael Figurnov, Olaf Ronneberger, Russ Bates, Simon A. A. Kohl, Anna Potapenko, Andrew J. Ballard, Bernardino Romera-Paredes, Stanislav Nikolov, Rishub Jain, Ellen Clancy, David Reiman, Stig Petersen, Andrew W. Senior, Koray Kavukcuoglu, Pushmeet Kohli, John Jumper & Demis Hassabis

  2. European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK

    Sameer Velankar, Gerard J. Kleywegt, Alex Bateman & Ewan Birney

Corresponding authors

Correspondence to
Kathryn Tunyasuvunakool or John Jumper or Demis Hassabis.

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Tunyasuvunakool, K., Adler, J., Wu, Z. et al. Highly accurate protein structure prediction for the human proteome.
Nature (2021). https://doi.org/10.1038/s41586-021-03828-1

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  • DOI: https://doi.org/10.1038/s41586-021-03828-1

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