{"entity": "researcher", "timestamp": "2026-08-20T20:51:19.743Z", "family": "Schwede", "given": "Torsten", "initials": "T", "orcid": "0000-0003-2715-335X", "affiliations": ["Biozentrum, University of Basel, Basel, Switzerland.", "SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Basel, Switzerland."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce9338dc4e0f41c0b756280291b43516.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce9338dc4e0f41c0b756280291b43516"}}, "publications": [{"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"}, {"entity": "publication", "iuid": "ce8151a3d4364e10b9b7e6ae88536bd9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ce8151a3d4364e10b9b7e6ae88536bd9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ce8151a3d4364e10b9b7e6ae88536bd9"}}, "title": "Estimation of model accuracy in CASP13.", "authors": [{"family": "Cheng", "given": "Jianlin", "initials": "J", "orcid": "0000-0003-0305-2853", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/592fe493ad8243e4811859daa863e037.json"}}, {"family": "Choe", "given": "Myong-Ho", "initials": "MH"}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}, {"family": "Han", "given": "Kun-Sop", "initials": "KS", "orcid": "0000-0001-6320-6573", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42a00ce989f84c74bc12a0469c3f5ca6.json"}}, {"family": "Hou", "given": "Jie", "initials": "J"}, {"family": "Maghrabi", "given": "Ali H A", "initials": "AHA"}, {"family": "McGuffin", "given": "Liam J", "initials": "LJ", "orcid": "0000-0003-4501-4767", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/486e6581ed0f49c3bbd3982356b1796e.json"}}, {"family": "Men\u00e9ndez-Hurtado", "given": "David", "initials": "D"}, {"family": "Olechnovi\u010d", "given": "Kliment", "initials": "K"}, {"family": "Schwede", "given": "Torsten", "initials": "T", "orcid": "0000-0003-2715-335X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce9338dc4e0f41c0b756280291b43516.json"}}, {"family": "Studer", "given": "Gabriel", "initials": "G"}, {"family": "Uziela", "given": "Karolis", "initials": "K", "orcid": "0000-0003-2232-3006", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28076573d34d421eaac36fcd344e7c36.json"}}, {"family": "Venclovas", "given": "\u010ceslovas", "initials": "\u010c", "orcid": "0000-0002-4215-0213", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/da101846338342de9dbebb21c95d896e.json"}}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-3772-8279", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/330342e0d01d4a0683bd6bda49064c21.json"}}], "type": "journal article", "published": "2019-12-00", "journal": {"title": "Proteins", "issn": "1097-0134", "volume": "87", "issue": "12", "pages": "1361-1377", "issn-l": "0887-3585"}, "abstract": "Methods to reliably estimate the accuracy of 3D models of proteins are both a fundamental part of most protein folding pipelines and important for reliable identification of the best models when multiple pipelines are used. Here, we describe the progress made from CASP12 to CASP13 in the field of estimation of model accuracy (EMA) as seen from the progress of the most successful methods in CASP13. We show small but clear progress, that is, several methods perform better than the best methods from CASP12 when tested on CASP13 EMA targets. Some progress is driven by applying deep learning and residue-residue contacts to model accuracy prediction. We show that the best EMA methods select better models than the best servers in CASP13, but that there exists a great potential to improve this further. Also, according to the evaluation criteria based on local similarities, such as lDDT and CAD, it is now clear that single model accuracy methods perform relatively better than consensus-based methods.", "doi": "10.1002/prot.25767", "pmid": "31265154", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1045720"}, {"db": "pmc", "key": "PMC6851425"}], "notes": [], "created": "2026-08-20T06:35:16.590Z", "modified": "2026-08-20T06:35:16.873Z"}]}