ArticleScience advances2025
The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes.
Article in Science advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Evolving strategies for virus discovery.Microbial genomics · 2026Review
- Computational prediction resolves thousands of homooligomeric phage protein structures.bioRxiv : the preprint server for biology · 2026Article
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- Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.Nucleic acids research · 2026Article
- Protein structure-informed bacteriophage genome annotation with Phold.Nucleic acids research · 2026Article
- Recent advances in the inference of deep viral evolutionary history.Journal of virology · 2025Review
- Fold first, ask later: structure-informed function annotation ofbioRxiv : the preprint server for biology · 2025Article
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Authors and funding
10 authors.
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Abstract
Viruses are the most abundant and genetically diverse entities on Earth, yet the functions and evolution of most viral proteins remain poorly understood. Their rapid evolution often obscures evolutionary relationships, limiting the ability to assign functions using sequence-based methods. Although the conservation of protein fold can reveal deep homologies, viral proteins remain underrepresented in structural databases. We address this by clustering viral sequences from RefSeq and predicting the structures of ~27,000 representative proteins using AlphaFold2 to create the Viral AlphaFold Database (VAD). We uncover conserved folds in diverse viruses infecting bacteria, archaea, and eukaryotes. We predict homodimers and make comparisons to the Protein Data Bank, providing data on oligomerization potential. We reveal considerable functional darkness in the viral protein universe and report the discovery and validation of an uncharacterized toxin-antitoxin system. The VAD provides a foundation for exploring viral structure-function relationships, including ancient folds shaping viral interactions across all life.
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