Exploring structural diversity across the protein universe with The Encyclopedia of Domains.

Journal: Science (New York, N.Y.)
PMID: 39480926

Abstract

The AlphaFold Protein Structure Database (AFDB) contains more than 214 million predicted protein structures composed of domains, which are independently folding units found in multiple structural and functional contexts. Identifying domains can enable many functional and evolutionary analyses but has remained challenging because of the sheer scale of the data. Using deep learning methods, we have detected and classified every domain in the AFDB, producing The Encyclopedia of Domains. We detected nearly 365 million domains, over 100 million more than can be found by sequence methods, covering more than 1 million taxa. Reassuringly, 77% of the nonredundant domains are similar to known superfamilies, greatly expanding representation of their domain space. We uncovered more than 10,000 new structural interactions between superfamilies and thousands of new folds across the fold space continuum.

Authors

  • Andy M Lau
    Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
  • Nicola Bordin
    Institute of Structural and Molecular Biology, University College London, Gower St, WC1E 6BT London, UK.
  • Shaun M Kandathil
    Department of Computer Science, University College London, London, UK.
  • Ian Sillitoe
    Institute of Structural and Molecular Biology, University College London, London, UK.
  • Vaishali P Waman
    Institute of Structural and Molecular Biology, University College London, London, UK.
  • Jude Wells
    Centre for Artificial Intelligence, University College London, WC1E 6BT, United Kingdom.
  • Christine A Orengo
    Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
  • David T Jones
    Department of Computer Science, Bioinformatics Group, University College London, Gower Street, London, WC1E 6BT, United Kingdom. d.t.jones@ucl.ac.uk.

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