Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes

  1. Yewon Han
  2. Riya Narain
  3. Razan Abbara
  4. Marcelo Querino Lima Afonso
  5. Jeannie Austin
  6. Damian Bertoni
  7. Sooyoung Cha
  8. Alexander I. Cowen-Rivers
  9. Joseph Ellaway
  10. Davide Fransos
  11. Kyle Gion
  12. Darren Hsu
  13. Chantal Hulo
  14. Rachel Seongeun Kim
  15. Oleg Kovalevskiy
  16. Agata Laydon
  17. Jack Mason
  18. Sreenath Nair
  19. Urmila Paramval
  20. Nilkanth Patel
  21. Risha Patel
  22. Ivanna Pidruchna
  23. Jeremy Ratcliff
  24. Maxim Tsenkov
  25. Niccolò Alberto Elia Venanzi
  26. Melanie Vollmar
  27. Newton Wahome
  28. Elisa L.H. Wong
  29. Jennifer Fleming
  30. Sameer Velankar
  31. Milot Mirdita
  32. Philippe Le Mercier
  33. Martin Steinegger
  34. Christian Dallago
  35. Joe Grove
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Abstract

Mechanistic understanding of viral protein-protein interactions enables global health security and pandemic preparedness, yet experimental characterisation remains difficult, costly, and often restricted to specialised laboratories. Here, we describe an in silico campaign using AlphaFold2 and AlphaFold-Multimer to predict monomers and dimer structures within 2,812 viral proteomes from 23 viral families relevant to human health. We report high-confidence predicted structures of 5,279 hetero-, and 2,749 homo-dimers. Structural clustering of interfaces reduces the set fivefold to 1,598 consolidated by form and function, of which 471 (29.5%) lacked detectable similarity to experimentally determined interfaces in the PDB. These clusters yielded two notable findings: new data on vaccinology-relevant glycoproteins, and accurate prediction of the specificity and cleavage-site recognition of viral proteases, which are targets for anti-viral development. Viral monomers and high-confidence dimers are available for interactive browsing in the Pandemic Preparedness Portal of the AlphaFold Database ( https://alphafold.ebi.ac.uk/ ), and the full dataset is available for bulk download.

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  1. Mentioned by @evbc.bsky.social on Bluesky

    🦠How do virus proteins interact to drive infection?Researchers used AlphaFold2 and AlphaFold-Multimer to predict thousands of protein dimers across 2,812 virus proteomes, revealing potential targets for antiviral development and vaccine research🔬 📄 doi.org/10.64898/202... 👤 EVBC: Philippe Le Mercier

  2. Mentioned by @danielhurdiss.bsky.social on Bluesky

    Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes www.biorxiv.org/content/10.6...

  3. Mentioned by @biorxiv-bioinfo.bsky.social on Bluesky

    Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes https://www.biorxiv.org/content/10.64898/2026.09.29.755321v1

  4. Mentioned by @biorxivpreprint.bsky.social on Bluesky

    Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes https://www.biorxiv.org/content/10.64898/2026.09.29.755321v1

  5. Version published to 10.64898/2026.09.29.755321v1 on bioRxiv