{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T06:53:59Z","timestamp":1792306439094,"version":"4.4.0"},"reference-count":94,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T00:00:00Z","timestamp":1767744000000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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\u00a0https:\/\/github.com\/gbouras13\/phold.<\/jats:p>","DOI":"10.1093\/nar\/gkaf1448","type":"journal-article","created":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T12:35:29Z","timestamp":1765197329000},"source":"Crossref","is-referenced-by-count":74,"title":["Protein structure-informed bacteriophage genome annotation with Phold"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5885-4186","authenticated-orcid":false,"given":"George","family":"Bouras","sequence":"first","affiliation":[{"name":"Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide , Adelaide, 5005 ,","place":["Australia"]},{"name":"The Department of Surgery\u2014Otolaryngology Head and Neck Surgery, Central Adelaide Local Health Network , Adelaide, 5000 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4738-3451","authenticated-orcid":false,"given":"Susanna R","family":"Grigson","sequence":"additional","affiliation":[{"name":"College of Science and Engineering, Flinders University , Bedford Park, 5042 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Milot","family":"Mirdita","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Seoul National University , Seoul ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Heinzinger","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Center , Munich, 85764 ,","place":["Germany"]},{"name":"TUM School of Computation, Information and Technology, Technical University of Munich , Munich, 85748 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5359-3100","authenticated-orcid":false,"given":"Bhavya","family":"Papudeshi","sequence":"additional","affiliation":[{"name":"College of Science and Engineering, Flinders University , Bedford Park, 5042 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vijini","family":"Mallawaarachchi","sequence":"additional","affiliation":[{"name":"College of Science and Engineering, Flinders University , Bedford Park, 5042 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Renee","family":"Green","sequence":"additional","affiliation":[{"name":"College of Science and Engineering, Flinders University , Bedford Park, 5042 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel Seongeun","family":"Kim","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Seoul National University , Seoul ,","place":["Republic of Korea"]},{"name":"Interdisciplinary Program in Bioinformatics, Seoul National University , Seoul ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor","family":"Mihalia","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Seoul National University , Seoul ,","place":["Republic of Korea"]},{"name":"Interdisciplinary Program in Bioinformatics, Seoul National University , Seoul ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alkis James","family":"Psaltis","sequence":"additional","affiliation":[{"name":"Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide , Adelaide, 5005 ,","place":["Australia"]},{"name":"The Department of Surgery\u2014Otolaryngology Head and Neck Surgery, Central Adelaide Local Health Network , Adelaide, 5000 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