{"entity": "researcher", "timestamp": "2026-08-20T20:57:31.688Z", "family": "Abdullah", "given": "Minhal", "initials": "M", "orcid": "0000-0002-6018-314X", "affiliations": ["Institute of Technology, University of Tartu, Tartu, Estonia.", "Department of Experimental Medical Science, Lund University, Lund, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c8fb279f2df41d2a5d86e7afbab9592.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c8fb279f2df41d2a5d86e7afbab9592"}}, "publications": [{"entity": "publication", "iuid": "d5dd1820f3d64bba98b64bc4c1396191", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d5dd1820f3d64bba98b64bc4c1396191.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d5dd1820f3d64bba98b64bc4c1396191"}}, "title": "The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes.", "authors": [{"family": "Odai", "given": "Roni", "initials": "R", "orcid": "0009-0002-2280-3915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/604a6d6e3cdb468d8c6acfb6a2e45ff9.json"}}, {"family": "Leemann", "given": "Mich\u00e8le", "initials": "M", "orcid": "0009-0008-9641-8837", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/124f42d408ce4e23aa91f3d82ab73f22.json"}}, {"family": "Al-Murad", "given": "Tamim", "initials": "T", "orcid": "0009-0009-9450-6734", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/09af3a6db1304f58ba96542af779c538.json"}}, {"family": "Abdullah", "given": "Minhal", "initials": "M", "orcid": "0000-0002-6018-314X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c8fb279f2df41d2a5d86e7afbab9592.json"}}, {"family": "Shyrokova", "given": "Lena", "initials": "L", "orcid": "0000-0002-0361-6359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9e14037d4da48408ecfa16d12742d1f.json"}}, {"family": "Tenson", "given": "Tanel", "initials": "T", "orcid": "0000-0002-0260-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44fd1d5f2b4f43c0a2067d75306c85ed.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}, {"family": "Durairaj", "given": "Janani", "initials": "J", "orcid": "0000-0002-1698-4556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbc37e3024a34e18b93c50bd7ce6c3a7.json"}}, {"family": "Pereira", "given": "Joana", "initials": "J", "orcid": "0000-0002-5588-6588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18123de080c84f7fba8ca71f1f294773.json"}}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC", "orcid": "0000-0002-4861-4584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8.json"}}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "40", "pages": "eadz8560", "issn-l": "2375-2548"}, "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.", "doi": "10.1126/sciadv.adz8560", "pmid": "41032608", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12487901"}], "notes": [], "created": "2026-08-20T11:59:12.908Z", "modified": "2026-08-20T11:59:13.115Z"}, {"entity": "publication", "iuid": "e0d872b5ec224de6822fcf82082b759a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e0d872b5ec224de6822fcf82082b759a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e0d872b5ec224de6822fcf82082b759a"}}, "title": "Uncovering new families and folds in the natural protein universe.", "authors": [{"family": "Durairaj", "given": "Janani", "initials": "J", "orcid": "0000-0002-1698-4556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbc37e3024a34e18b93c50bd7ce6c3a7.json"}}, {"family": "Waterhouse", "given": "Andrew M", "initials": "AM", "orcid": "0009-0004-5717-6063", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acfd68ed308a4b39971d70a1d48adc09.json"}}, {"family": "Mets", "given": "Toomas", "initials": "T"}, {"family": "Brodiazhenko", "given": "Tetiana", "initials": "T"}, {"family": "Abdullah", "given": "Minhal", "initials": "M", "orcid": "0000-0002-6018-314X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c8fb279f2df41d2a5d86e7afbab9592.json"}}, {"family": "Studer", "given": "Gabriel", "initials": "G"}, {"family": "Tauriello", "given": "Gerardo", "initials": "G", "orcid": "0000-0002-5921-7007", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2bb2e6461c040f59429b6d8bd838523.json"}}, {"family": "Akdel", "given": "Mehmet", "initials": "M"}, {"family": "Andreeva", "given": "Antonina", "initials": "A", "orcid": "0000-0002-0450-0091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3c34ecb82054acfa7ead18dd8882f39.json"}}, {"family": "Bateman", "given": "Alex", "initials": "A", "orcid": "0000-0002-6982-4660", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01e1775e560147c2b7c40e1ba7d95a4e.json"}}, {"family": "Tenson", "given": "Tanel", "initials": "T", "orcid": "0000-0002-0260-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44fd1d5f2b4f43c0a2067d75306c85ed.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}, {"family": "Schwede", "given": "Torsten", "initials": "T", "orcid": "0000-0003-2715-335X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce9338dc4e0f41c0b756280291b43516.json"}}, {"family": "Pereira", "given": "Joana", "initials": "J", "orcid": "0000-0002-5588-6588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18123de080c84f7fba8ca71f1f294773.json"}}], "type": "journal article", "published": "2023-10-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "622", "issue": "7983", "pages": "646-653", "issn-l": "0028-0836"}, "abstract": "We are now entering a new era in protein sequence and structure annotation, with hundreds of millions of predicted protein structures made available through the AlphaFold database1. These models cover nearly all proteins that are known, including those challenging to annotate for function or putative biological role using standard homology-based approaches. In this study, we examine the extent to which the AlphaFold database has structurally illuminated this 'dark matter' of the natural protein universe at high predicted accuracy. We further describe the protein diversity that these models cover as an annotated interactive sequence similarity network, accessible at https://uniprot3d.org/atlas/AFDB90v4 . By searching for novelties from sequence, structure and semantic perspectives, we uncovered the \u03b2-flower fold, added several protein families to Pfam database2 and experimentally demonstrated that one of these belongs to a new superfamily of translation-targeting toxin-antitoxin systems, TumE-TumA. This work underscores the value of large-scale efforts in identifying, annotating and prioritizing new protein families. By leveraging the recent deep learning revolution in protein bioinformatics, we can now shed light into uncharted areas of the protein universe at an unprecedented scale, paving the way to innovations in life sciences and biotechnology.", "doi": "10.1038/s41586-023-06622-3", "pmid": "37704037", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10584680"}, {"db": "pii", "key": "10.1038/s41586-023-06622-3"}], "notes": [], "created": "2026-08-20T08:58:40.431Z", "modified": "2026-08-20T08:58:40.772Z"}, {"entity": "publication", "iuid": "740732b7f155421d92f9a2674081defb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/740732b7f155421d92f9a2674081defb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/740732b7f155421d92f9a2674081defb"}}, "title": "What is hidden in the darkness? Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds", "authors": [{"family": "Durairaj", "given": "Janani", "initials": "J", "orcid": "0000-0002-1698-4556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbc37e3024a34e18b93c50bd7ce6c3a7.json"}}, {"family": "Waterhouse", "given": "Andrew M", "initials": "AM"}, {"family": "Mets", "given": "Toomas", "initials": "T", "orcid": "0000-0002-6796-7000", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7dbceebe30234575b3575ef4f44c0511.json"}}, {"family": "Brodiazhenko", "given": "Tetiana", "initials": "T"}, {"family": "Abdullah", "given": "Minhal", "initials": "M", "orcid": "0000-0002-6018-314X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c8fb279f2df41d2a5d86e7afbab9592.json"}}, {"family": "Studer", "given": "Gabriel", "initials": "G", "orcid": "0000-0003-0462-1456", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a063e4b2d8284a1486037652aa35b11b.json"}}, {"family": "Akdel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-6092-3494", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/adcc39b269804e179cbea223cc8dc83d.json"}}, {"family": "Andreeva", "given": "Antonina", "initials": "A", "orcid": "0000-0002-0450-0091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3c34ecb82054acfa7ead18dd8882f39.json"}}, {"family": "Bateman", "given": "Alex", "initials": "A", "orcid": "0000-0002-6982-4660", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01e1775e560147c2b7c40e1ba7d95a4e.json"}}, {"family": "Tenson", "given": "Tanel", "initials": "T", "orcid": "0000-0002-0260-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44fd1d5f2b4f43c0a2067d75306c85ed.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}, {"family": "Schwede", "given": "Torsten", "initials": "T", "orcid": "0000-0003-2715-335X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce9338dc4e0f41c0b756280291b43516.json"}}, {"family": "Pereira", "given": "Joana", "initials": "J", "orcid": "0000-0002-5588-6588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18123de080c84f7fba8ca71f1f294773.json"}}], "type": "posted-content", "published": "2023-03-15", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.03.14.532539", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:44:24.617Z", "modified": "2026-08-20T10:44:24.767Z"}]}