ArticleNucleic acids research2026
Protein structure-informed bacteriophage genome annotation with Phold.
Article in Nucleic acids research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Dental wastewater reveals a hidden reservoir of oral bacteriophage diversity.Microbiology spectrum · 2026Article
- The PhageExpressionAtlas reveals shared and unique transcriptional patterns across phage-host interactions.NAR genomics and bioinformatics · 2026Article
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- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- Chloramphenicol and tetracycline synergize with bacteriophage SeKF_13 to inactivate antimicrobial-resistantMicrobiology spectrum · 2026Article
- Characterization ofMicrobiology spectrum · 2026Article
- A genomic catalog of the mouse gut virome reveals features associated with ageing.Nature communications · 2026Article
- Viral genetic diversity and functional potential in polar and subarctic sea ice.FEMS microbiology ecology · 2026Article
- ProtPen combines sequence- and structure-based approaches to facilitate protein function predictions on a proteome-wide scale.bioRxiv : the preprint server for biology · 2026Article
- Genome sequence ofMicrobiology resource announcements · 2026Article
- Unraveling a new Klebsiella phage KP47 against Klebsiella spp.BMC microbiology · 2026Article
- Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and Phynteny.Current protocols · 2026Article
- Evolving strategies for virus discovery.Microbial genomics · 2026Review
- Complete genome sequence ofMicrobiology resource announcements · 2026Article
- Persistent trade-offs balance competition and colonization across centuries.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Ten quick tips for classifying unknown bacteriophage.PLoS computational biology · 2026Article
- Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.Science advances · 2026Article
- Isolation of novel phages from a resistant Dorea longicatena strain reveals genes associated with phage resistance.Npj viruses · 2026Article
- Computational prediction resolves thousands of homooligomeric phage protein structures.bioRxiv : the preprint server for biology · 2026Article
- The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome.Nature communications · 2026Article
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
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 utilizing 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 reveal 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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