{"entity": "researcher", "timestamp": "2026-08-20T21:01:44.710Z", "family": "Bassot", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7161-9028", "affiliations": ["Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 21 Solna, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd30fb53be1f49718ef8c71addd5802e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd30fb53be1f49718ef8c71addd5802e"}}, "publications": [{"entity": "publication", "iuid": "ecddf63436744689a1ed09649fa2610a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ecddf63436744689a1ed09649fa2610a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ecddf63436744689a1ed09649fa2610a"}}, "title": "DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.", "authors": [{"family": "Quaglia", "given": "Federica", "initials": "F", "orcid": "0000-0002-0341-4888", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6657e12ee16a450aaca2c23b04e5a283.json"}}, {"family": "M\u00e9sz\u00e1ros", "given": "B\u00e1lint", "initials": "B", "orcid": "0000-0003-0919-4449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f5847cba0f8f43e6b6827a40ddf47f2c.json"}}, {"family": "Salladini", "given": "Edoardo", "initials": "E", "orcid": "0000-0002-5152-5953", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35587acab31f476eafa5885746e56477.json"}}, {"family": "Hatos", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0001-9224-9820", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c092bf996e3f4583835c054ab625bd82.json"}}, {"family": "Pancsa", "given": "Rita", "initials": "R", "orcid": "0000-0003-0849-9312", "researcher": {"href": 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"Nevena", "initials": "N", "orcid": "0000-0001-6562-5800", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7a1d0994c8fb42c5abf35b0e82884c18.json"}}, {"family": "Parisi", "given": "Gustavo", "initials": "G", "orcid": "0000-0001-7444-1624", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/014eb4c06cbe4597ad14afc5f9146f6a.json"}}, {"family": "Ventura", "given": "Salvador", "initials": "S", "orcid": "0000-0002-9652-6351", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e0afcd4cf084de6be1e2e606f6e954c.json"}}, {"family": "Doszt\u00e1nyi", "given": "Zsuzsanna", "initials": "Z", "orcid": "0000-0002-3624-5937", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77615a3783aa490ebc0dc300958ea70f.json"}}, {"family": "Tompa", "given": "Peter", "initials": "P", "orcid": "0000-0001-8042-9939", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57f930a048ce4e5b9d65c9d173bd9954.json"}}, {"family": "Tosatto", "given": "Silvio C E", "initials": "SCE", "orcid": "0000-0003-4525-7793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/152b8eca864e44f1954ee4952c60aa0d.json"}}, {"family": "Piovesan", "given": "Damiano", "initials": "D", "orcid": "0000-0001-8210-2390", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/994db11834b0446895c5cd4b28be1d8b.json"}}], "type": "journal article", "published": "2022-01-07", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "50", "issue": "D1", "pages": "D480-D487", "issn-l": "0305-1048"}, "abstract": "The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure.", "doi": "10.1093/nar/gkab1082", "pmid": "34850135", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8728214"}, {"db": "pii", "key": "6439667"}], "notes": [], "created": "2026-08-20T09:49:35.446Z", "modified": "2026-08-20T09:49:37.565Z"}, {"entity": "publication", "iuid": "32897143c456418484e1f8c88bed90f9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/32897143c456418484e1f8c88bed90f9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/32897143c456418484e1f8c88bed90f9"}}, "title": "The evolutionary history of topological variations in the CPA/AT transporters.", "authors": [{"family": "Sudha", "given": "Govindarajan", "initials": "G"}, {"family": "Bassot", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7161-9028", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd30fb53be1f49718ef8c71addd5802e.json"}}, {"family": "Lamb", "given": "John", "initials": "J", "orcid": "0000-0003-0568-8281", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab0a410bcea240c1b74301230b9fdfac.json"}}, {"family": "Shu", "given": "Nanjiang", "initials": "N", "orcid": "0000-0002-3537-2387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/678923f15c594ef685f353c42fdfc627.json"}}, {"family": "Huang", "given": "Yan", "initials": "Y"}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "volume": "17", "issue": "8", "pages": "e1009278", "issn-l": "1553-734X"}, "abstract": "CPA/AT transporters are made up of scaffold and a core domain. The core domain contains two non-canonical helices (broken or reentrant) that mediate the transport of ions, amino acids or other charged compounds. During evolution, these transporters have undergone substantial changes in structure, topology and function. To shed light on these structural transitions, we create models for all families using an integrated topology annotation method. We find that the CPA/AT transporters can be classified into four fold-types based on their structure; (1) the CPA-broken fold-type, (2) the CPA-reentrant fold-type, (3) the BART fold-type, and (4) a previously not described fold-type, the Reentrant-Helix-Reentrant fold-type. Several topological transitions are identified, including the transition between a broken and reentrant helix, one transition between a loop and a reentrant helix, complete changes of orientation, and changes in the number of scaffold helices. These transitions are mainly caused by gene duplication and shuffling events. Structural models, topology information and other details are presented in a searchable database, CPAfold (cpafold.bioinfo.se).", "doi": "10.1371/journal.pcbi.1009278", "pmid": "34403419", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8396727"}, {"db": "pii", "key": "PCOMPBIOL-D-20-02296"}, {"db": "figshare", "key": "10.6084/m9.figshare.14575626.v1"}], "notes": [], "created": "2026-08-20T12:43:03.815Z", "modified": "2026-08-20T12:43:03.893Z"}, {"entity": "publication", "iuid": "22e426feb67947dca555107b1d6ec680", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/22e426feb67947dca555107b1d6ec680.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/22e426feb67947dca555107b1d6ec680"}}, "title": "Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families.", "authors": [{"family": "Bassot", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7161-9028", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd30fb53be1f49718ef8c71addd5802e.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "volume": "17", "issue": "4", "pages": "e1008798", "issn-l": "1553-734X"}, "abstract": "Repeat proteins are abundant in eukaryotic proteomes. They are involved in many eukaryotic specific functions, including signalling. For many of these proteins, the structure is not known, as they are difficult to crystallise. Today, using direct coupling analysis and deep learning it is often possible to predict a protein's structure. However, the unique sequence features present in repeat proteins have been a challenge to use direct coupling analysis for predicting contacts. Here, we show that deep learning-based methods (trRosetta, DeepMetaPsicov (DMP) and PconsC4) overcomes this problem and can predict intra- and inter-unit contacts in repeat proteins. In a benchmark dataset of 815 repeat proteins, about 90% can be correctly modelled. Further, among 48 PFAM families lacking a protein structure, we produce models of forty-one families with estimated high accuracy.", "doi": "10.1371/journal.pcbi.1008798", "pmid": "33857128", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8078820"}, {"db": "pii", "key": "PCOMPBIOL-D-20-01386"}], "notes": [], "created": "2026-08-20T12:42:59.139Z", "modified": "2026-08-20T12:42:59.225Z"}, {"entity": "publication", "iuid": "114eac47e597481fa306ca759ceb4b0a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/114eac47e597481fa306ca759ceb4b0a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/114eac47e597481fa306ca759ceb4b0a"}}, "title": "Why do eukaryotic proteins contain more intrinsically disordered regions?", "authors": [{"family": "Basile", "given": "Walter", "initials": "W", "orcid": "0000-0003-1701-222X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e6578ab5c97746049172b4b4a8b93414.json"}}, {"family": "Salvatore", "given": "Marco", "initials": "M"}, {"family": "Bassot", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7161-9028", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd30fb53be1f49718ef8c71addd5802e.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "journal article", "published": "2019-07-00", "journal": {"title": "PLoS Comput Biol", "issn": "1553-7358", "volume": "15", "issue": "7", "pages": "e1007186", "issn-l": "1553-734X"}, "abstract": "Intrinsic disorder is more abundant in eukaryotic than prokaryotic proteins. Methods predicting intrinsic disorder are based on the amino acid sequence of a protein. Therefore, there must exist an underlying difference in the sequences between eukaryotic and prokaryotic proteins causing the (predicted) difference in intrinsic disorder. By comparing proteins, from complete eukaryotic and prokaryotic proteomes, we show that the difference in intrinsic disorder emerges from the linker regions connecting Pfam domains. Eukaryotic proteins have more extended linker regions, and in addition, the eukaryotic linkers are significantly more disordered, 38% vs. 12-16% disordered residues. Next, we examined the underlying reason for the increase in disorder in eukaryotic linkers, and we found that the changes in abundance of only three amino acids cause the increase. Eukaryotic proteins contain 8.6% serine; while prokaryotic proteins have 6.5%, eukaryotic proteins also contain 5.4% proline and 5.3% isoleucine compared with 4.0% proline and \u2248 7.5% isoleucine in the prokaryotes. All these three differences contribute to the increased disorder in eukaryotic proteins. It is tempting to speculate that the increase in serine frequencies in eukaryotes is related to regulation by kinases, but direct evidence for this is lacking. The differences are observed in all phyla, protein families, structural regions and type of protein but are most pronounced in disordered and linker regions. The observation that differences in the abundance of three amino acids cause the difference in disorder between eukaryotic and prokaryotic proteins raises the question: Are amino acid frequencies different in eukaryotic linkers because the linkers are more disordered or do the differences cause the increased disorder?", "doi": "10.1371/journal.pcbi.1007186", "pmid": "31329574", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6675126"}, {"db": "pii", "key": "PCOMPBIOL-D-18-02156"}], "notes": [], "created": "2026-08-20T12:42:49.703Z", "modified": "2026-08-20T12:42:49.791Z"}]}