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PreprintCited by 71Bacteriophages and microbial interactionsGenomics and Phylogenetic StudiesProtein Structure and Dynamics

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Protein Structure Informed Bacteriophage Genome Annotation with Phold

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Bouras, George, Grigson, Susanna R., Mirdita, Milot, Heinzinger, Michael, Papudeshi, Bhavya, Mallawaarachchi, Vijini, Green, Renee, Kim, Rachel Seongeun, Mihalia, Victor, Psaltis, Alkis James, Wormald, Peter-John, Vreugde, Sarah, Steinegger, Martin, Edwards, Robert A.·2025·Nucleic Acids Research
DOI 10.1101/2025.08.05.668817PMC PMC12774648

Preprint — published as 10.1093/nar/gkaf1448 · Paper page

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Abstract

Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilising protein structural information that combines the ProstT5 protein language model and structural alignment tool Foldseek. Phold assigns annotations using a database of over 1.36 million predicted phage protein structures with high quality functional labels. Benchmarking reveals that Phold outperforms existing sequence-based homology approaches in functional annotation sensitivity whilst maintaining speed, consistency and scalability. Applying Phold to diverse cultured and metagenomic phage genomes shows it consistently annotates over 50% of genes on an average phage and 40% on an average archaeal virus. Comparisons of phage protein structures to other protein structures across the tree of life reveals that phage proteins commonly have structural homology to proteins shared across the tree of life, particularly those that have nucleic acid metabolism and enzymatic functions. Phold is available as free and open-source software at https://github.com/gbouras13/phold .

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Metadata

Authors
Bouras, G., Grigson, S. R., Mirdita, M., Heinzinger, M., Papudeshi, B., Mallawaarachchi, V., Green, R., Kim, R. S., Mihalia, V., Psaltis, A. J., Wormald, P.-J., Vreugde, S., Steinegger, M., & Edwards, R. A.
Affiliations
  • Central Adelaide Local Health Network (AU)
  • Flinders University (AU)
  • Seoul National University (KR)
  • Helmholtz Munich (DE)
Corresponding author
  • Bouras, George
  • Edwards, Robert A.
ORCID
Venue
Nucleic Acids Research
Publisher
openRxiv
Published
2025-08-06
Volume
54
Issue
1
ISSN
0305-1048 (ISSN-L)
DOI
10.1101/2025.08.05.668817
PMC
PMC12774648
OpenAlex
W7118953414
Cited by
71
References
2
Citations by year
2026: 63 · 2025: 8
FWCI
37.44
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion, cc-by)
  • Seoul National University Open Repository (Seoul National University) (submittedVersion)
Funders
  • National Research Foundation of Korea (2020M3A9G7103933, RS-2021-NR061659, RS-2021-NR056571, RS-2024-00396026, RS-2023-00250470)
  • Novo Nordisk Foundation (NNF24SA0092560)
  • Samsung DS Research Fund
  • Creative-Pioneering Researchers Program
  • AI-Bio Research Grant through Seoul National University
Topics
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
protein structural homology, Foldseek, functional annotation, archaeal viruses, structural alignment, phage therapy
MeSH terms
Bacteriophages, Software, Viral Proteins, Genome, Viral, Molecular Sequence Annotation

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