Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes
- 1University of Glasgow, UK.; MRC-University of Glasgow Centre for Virus Research, UK.
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.
Related
- Polyglutamine-expanded TBP rewires neuronal and muscle proteomes beyond transcription in a Drosophila model of SCA17
- Network analysis of mouse brain proteomes resolves molecular and cellular endophenotypes of aging and Aβ pathology
- Enhanced Antimicrobial Potency and Therapeutic Index of a Defined C12 Quaternary Ammonium Compound
- Analysis of 515 human proteomes defines plasma extracellular vesicle core composition, corona and coisolated networks
- Early terminated transcripts and missing proteins reflect artifacts in bacterial proteomes
BibTeX
@misc{han2026systematic,
title = {{Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes}},
author = {Y. Han and R. Narain and R. Abbara and M. Q. L. Afonso and J. Austin and D. Bertoni and S. Cha and A. I. Cowen-Rivers and J. I. J. Ellaway and D. Fransos and K. Gion and D. Hsu and C. Hulo and R. S. Kim and O. Kovalevskiy and A. Laydon and J. Mason and S. Nair and U. Paramval and N. Patel and R. Patel and I. Pidruchna and J. Ratcliff and M. I. Tsenkov and N. A. E. Vanenzi and M. Vollmar and N. Wahome and E. L. H. Wong and J. R. Fleming and S. Velankar and M. Mirdita and P. Le Mercier and M. Steinegger and C. Dallago and J. Grove},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.29.755321},
url = {https://www.biorxiv.org/content/10.64898/2026.09.29.755321v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes
AU - Y. Han
AU - R. Narain
AU - R. Abbara
AU - M. Q. L. Afonso
AU - J. Austin
AU - D. Bertoni
AU - S. Cha
AU - A. I. Cowen-Rivers
AU - J. I. J. Ellaway
AU - D. Fransos
AU - K. Gion
AU - D. Hsu
AU - C. Hulo
AU - R. S. Kim
AU - O. Kovalevskiy
AU - A. Laydon
AU - J. Mason
AU - S. Nair
AU - U. Paramval
AU - N. Patel
AU - R. Patel
AU - I. Pidruchna
AU - J. Ratcliff
AU - M. I. Tsenkov
AU - N. A. E. Vanenzi
AU - M. Vollmar
AU - N. Wahome
AU - E. L. H. Wong
AU - J. R. Fleming
AU - S. Velankar
AU - M. Mirdita
AU - P. Le Mercier
AU - M. Steinegger
AU - C. Dallago
AU - J. Grove
PY - 2026
DA - 2026/09/29
PB - bioRxiv
DO - 10.64898/2026.09.29.755321
UR - https://www.biorxiv.org/content/10.64898/2026.09.29.755321v1
AB - 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.
ER -