{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,26]],"date-time":"2026-01-26T03:41:43Z","timestamp":1769398903627,"version":"3.49.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2025,10,15]],"date-time":"2025-10-15T00:00:00Z","timestamp":1760486400000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009559","name":"Universidad Nacional de Quilmes","doi-asserted-by":"publisher","award":["PUNQ 2282\/22"],"award-info":[{"award-number":["PUNQ 2282\/22"]}],"id":[{"id":"10.13039\/501100009559","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003074","name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica [ANPCyT","doi-asserted-by":"crossref","award":["PICT 2018-03190"],"award-info":[{"award-number":["PICT 2018-03190"]}],"id":[{"id":"10.13039\/501100003074","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100003074","name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica [ANPCyT","doi-asserted-by":"crossref","award":["PICT 2020-2195"],"award-info":[{"award-number":["PICT 2020-2195"]}],"id":[{"id":"10.13039\/501100003074","id-type":"DOI","asserted-by":"crossref"}]},{"name":"European Union [Horizon Europe MSCA SE","award":["101182949"],"award-info":[{"award-number":["101182949"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Liquid\u2013liquid phase separation (LLPS) is a key process underlying the formation of biomolecular condensates, such as membrane-less organelles, that compartmentalize biochemical processes inside the cells. While LLPS has been extensively studied in eukaryotes, its role in bacteria, archaea, and viruses remains far less characterized. Recent studies in bacteria have revealed that LLPS-driven condensates play critical roles in RNA processing, stress response, and pathogenicity. Similarly, many viruses exploit LLPS to facilitate crucial steps in their infection cycles, including viral entry, genome replication, assembly, and host immune evasion.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this work, we introduce a hand-curated database of LLPS proteins from bacteria, archaea, and viruses (BAV-LLPS Database). This resource, extended through sequence similarity searches, comprises over 5000 proteins and integrates diverse data including biological annotations, sequence features, predicted disordered regions, LLPS per site probability, and AlphaFold2-based structural models. Additionally, our web server enables users to explore both the curated and homologous derived datasets, providing a platform to uncover evolutionary relationships and intrinsic and differential properties of LLPS proteins across various taxonomic groups. This work seeks to deepen our understanding of LLPS mechanisms beyond eukaryotic organisms, emphasizing their significance across diverse life forms. It also aims to foster the development of specialized predictive tools that will facilitate the exploration and characterization of LLPS processes in a wide array of living organisms, thereby contributing to advancements in both fundamental biological research and applied biomedical sciences.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>BAV-LLPS DB is freely accessible at https:\/\/bav-llps-db.bioinformatica.org\/. The data can be retrieved from the website. The source code of the database can be downloaded from https:\/\/bav-llps-db.bioinformatica.org\/download.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf550","type":"journal-article","created":{"date-parts":[[2025,10,15]],"date-time":"2025-10-15T20:31:16Z","timestamp":1760560276000},"source":"Crossref","is-referenced-by-count":1,"title":["BAV-LLPS: a database of bacterial, archaea, and virus liquid\u2013liquid phase separation proteins"],"prefix":"10.1093","volume":"41","author":[{"given":"Cecilia B","family":"Rodriguez","sequence":"first","affiliation":[{"name":"Departamento de Ciencia y Tecnolog\u00eda, Universidad Nacional de Quilmes , Bernal B1876BXD,","place":["Argentina"]}]},{"given":"Ronaldo Romario","family":"Tunque Cahui","sequence":"additional","affiliation":[{"name":"Department of Engineering, Faculty of Science and Engineering, Pontifical Catholic University of Peru , Lima 15088, Peru"}]},{"given":"Nicolas","family":"Demitroff","sequence":"additional","affiliation":[{"name":"Departamento de Ciencia y Tecnolog\u00eda, Universidad Nacional de Quilmes , Bernal B1876BXD,","place":["Argentina"]}]},{"given":"Layla","family":"Hirsh","sequence":"additional","affiliation":[{"name":"Department of Engineering, Faculty of Science and Engineering, Pontifical Catholic University of Peru , Lima 15088, Peru"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9453-4753","authenticated-orcid":false,"given":"Damien P","family":"Devos","sequence":"additional","affiliation":[{"name":"Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019\u2014UMR 9017\u2014CIIL\u2014Center for Infection and Immunity of Lille , Lille F-59000,","place":["France"]}]},{"given":"Graciela","family":"Boccaccio","sequence":"additional","affiliation":[{"name":"Fundaci\u00f3n Instituto Leloir (FIL)\u2014Instituto de Investigaciones Bioqu\u00edmicas de Buenos Aires (IIBBA)\u2014Consejo Nacional de Investigaciones Cient\u00edficas y Tecnol\u00f3gicas (CONICET) , Buenos Aires C1405BWE,","place":["Argentina"]},{"name":"Department of Molecular and Cellular Biology and Physiology (FBMyC), Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires (UBA) , Buenos Aires C1428EHA,","place":["Argentina"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7444-1624","authenticated-orcid":false,"given":"Gustavo","family":"Parisi","sequence":"additional","affiliation":[{"name":"Departamento de Ciencia y Tecnolog\u00eda, Universidad Nacional de Quilmes , Bernal B1876BXD,","place":["Argentina"]}]}],"member":"286","published-online":{"date-parts":[[2025,10,15]]},"reference":[{"key":"2025101710111408200_btaf550-B1","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1016\/j.molcel.2020.04.001","article-title":"BR-bodies provide selectively permeable condensates that stimulate mRNA decay and prevent release of decay intermediates","volume":"78","author":"Al-Husini","year":"2020","journal-title":"Mol Cell"},{"key":"2025101710111408200_btaf550-B2","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1016\/j.molcel.2018.08.003","article-title":"\u03b1-proteobacterial RNA degradosomes assemble liquid\u2013liquid phase-separated RNP bodies","volume":"71","author":"Al-Husini","year":"2018","journal-title":"Mol Cell"},{"key":"2025101710111408200_btaf550-B3","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1146\/annurev-genet-112618-043527","article-title":"Liquid\u2013liquid phase separation in disease","volume":"53","author":"Alberti","year":"2019","journal-title":"Annu Rev Genet"},{"key":"2025101710111408200_btaf550-B4","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1016\/j.bpj.2020.09.023","article-title":"The emergence of phase separation as an organizing principle in bacteria","volume":"120","author":"Azaldegui","year":"2021","journal-title":"Biophys J"},{"key":"2025101710111408200_btaf550-B5","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1126\/science.1257037","article-title":"Influenza a virus uses the aggresome processing machinery for host cell entry","volume":"346","author":"Banerjee","year":"2014","journal-title":"Science"},{"key":"2025101710111408200_btaf550-B6","doi-asserted-by":"crossref","first-page":"168803","DOI":"10.1016\/j.jmb.2024.168803","article-title":"Thermostable nucleoid protein Cren7 slides along DNA and rapidly dissociates from DNA while not inhibiting the sliding of other DNA-binding protein","volume":"436","author":"Banerjee","year":"2024","journal-title":"J Mol Biol"},{"key":"2025101710111408200_btaf550-B7","doi-asserted-by":"crossref","first-page":"167976","DOI":"10.1016\/j.jmb.2023.167976","article-title":"Membraneless organelles and condensates orchestrate innate immunity against viruses","volume":"435","author":"Boccaccio","year":"2023","journal-title":"J Mol Biol"},{"key":"2025101710111408200_btaf550-B8","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/B978-0-12-823967-4.00002-6","volume-title":"Droplets of Life","author":"Darling","year":"2023"},{"key":"2025101710111408200_btaf550-B9","doi-asserted-by":"crossref","first-page":"W176","DOI":"10.1093\/nar\/gkae385","article-title":"AIUPred: combining energy estimation with deep learning for the enhanced prediction of protein disorder","volume":"52","author":"Erd\u0151s","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025101710111408200_btaf550-B10","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/B978-0-12-823967-4.00005-1","volume-title":"Droplets of Life","author":"Fern\u00e1ndez-Alvarez","year":"2023"},{"key":"2025101710111408200_btaf550-B11","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1042\/EBC20220052","article-title":"Biological soft matter: intrinsically disordered proteins in liquid\u2013liquid phase separation and biomolecular condensates","volume":"66","author":"Fonin","year":"2022","journal-title":"Essays Biochem"},{"key":"2025101710111408200_btaf550-B12","doi-asserted-by":"crossref","first-page":"102706","DOI":"10.1016\/j.sbi.2023.102706","article-title":"Viral amyloids: new opportunities for antiviral therapeutic strategies","volume":"83","author":"Gondelaud","year":"2023","journal-title":"Curr Opin Struct Biol"},{"key":"2025101710111408200_btaf550-B13","doi-asserted-by":"crossref","first-page":"33254","DOI":"10.1073\/pnas.2007670117","article-title":"Widespread occurrence of the droplet state of proteins in the human proteome","volume":"117","author":"Hardenberg","year":"2020","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025101710111408200_btaf550-B14","doi-asserted-by":"crossref","first-page":"eabh2929","DOI":"10.1126\/sciadv.abh2929","article-title":"Membraneless organelles formed by liquid\u2013liquid phase separation increase bacterial fitness","volume":"7","author":"Jin","year":"2021","journal-title":"Sci Adv"},{"key":"2025101710111408200_btaf550-B15","doi-asserted-by":"crossref","first-page":"1149","DOI":"10.1126\/science.abn7229","article-title":"Bacteria require phase separation for fitness in the mammalian gut","volume":"379","author":"Krypotou","year":"2023","journal-title":"Science"},{"key":"2025101710111408200_btaf550-B16","doi-asserted-by":"crossref","first-page":"6582","DOI":"10.3390\/molecules28186582","article-title":"Liquid\u2013liquid phase separation and protective protein aggregates in bacteria","volume":"28","author":"Kuczy\u0144ska-Wi\u015bnik","year":"2023","journal-title":"Molecules"},{"key":"2025101710111408200_btaf550-B17","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1016\/j.it.2024.04.009","article-title":"Liquid\u2013liquid phase separation in innate immunity","volume":"45","author":"Liu","year":"2024","journal-title":"Trends Immunol"},{"key":"2025101710111408200_btaf550-B18","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.1016\/j.tim.2022.06.005","article-title":"Phase separation in viral infections","volume":"30","author":"Li","year":"2022","journal-title":"Trends Microbiol"},{"key":"2025101710111408200_btaf550-B19","doi-asserted-by":"crossref","first-page":"D320","DOI":"10.1093\/nar\/gkz778","article-title":"LLPSDB: a database of proteins undergoing liquid\u2013liquid phase separation in vitro","volume":"48","author":"Li","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025101710111408200_btaf550-B20","doi-asserted-by":"crossref","first-page":"e1009926","DOI":"10.1371\/journal.ppat.1009926","article-title":"Deconstructing virus condensation","volume":"17","author":"Lopez","year":"2021","journal-title":"PLoS Pathog"},{"key":"2025101710111408200_btaf550-B21","first-page":"133:jcs237057","article-title":"Bacterial cell division at a glance","author":"Mahone","year":"2020","journal-title":"J Cell Sci"},{"key":"2025101710111408200_btaf550-B22","first-page":"D360","article-title":"PhaSePro: the database of proteins driving liquid\u2013liquid phase separation","volume":"48","author":"M\u00e9sz\u00e1ros","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025101710111408200_btaf550-B23","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41592-022-01488-1","article-title":"ColabFold: making protein folding accessible to all","volume":"19","author":"Mirdita","year":"2022","journal-title":"Nat Methods"},{"key":"2025101710111408200_btaf550-B24","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/s13059-025-03497-7","article-title":"catGRANULE 2.0: accurate predictions of liquid\u2013liquid phase separating proteins at single amino acid resolution","volume":"26","author":"Monti","year":"2025","journal-title":"Genome Biol"},{"key":"2025101710111408200_btaf550-B25","doi-asserted-by":"crossref","first-page":"D288","DOI":"10.1093\/nar\/gkz1027","article-title":"DrLLPS: a data resource of liquid\u2013liquid phase separation in eukaryotes","volume":"48","author":"Ning","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025101710111408200_btaf550-B26","doi-asserted-by":"crossref","first-page":"e4858","DOI":"10.1002\/pro.4858","article-title":"MLOsMetaDB, a meta-database to centralize the information on liquid\u2013liquid phase separation proteins and membraneless organelles","volume":"33","author":"Orti","year":"2024","journal-title":"Protein Sci"},{"key":"2025101710111408200_btaf550-B27","doi-asserted-by":"crossref","first-page":"e4466","DOI":"10.1002\/pro.4466","article-title":"Intrinsic protein disorder and conditional folding in AlphaFoldDB","volume":"31","author":"Piovesan","year":"2022","journal-title":"Protein Sci"},{"key":"2025101710111408200_btaf550-B28","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/j.molcel.2018.10.022","article-title":"ATP-dependent dynamic protein aggregation regulates bacterial dormancy depth critical for antibiotic tolerance","volume":"73","author":"Pu","year":"2019","journal-title":"Mol Cell"},{"key":"2025101710111408200_btaf550-B29","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1038\/s42003-023-04963-3","article-title":"Biomolecular condensates\u2014extant relics or evolving microcompartments?","volume":"6","author":"Rangachari","year":"2023","journal-title":"Commun Biol"},{"key":"2025101710111408200_btaf550-B30","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1038\/s41592-023-01831-0","article-title":"CD-CODE: crowdsourcing condensate database and encyclopedia","volume":"20","author":"Rostam","year":"2023","journal-title":"Nat Methods"},{"key":"2025101710111408200_btaf550-B31","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1073\/pnas.2111696118","article-title":"Accurate model of liquid\u2013liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties","volume":"118","author":"Tesei","year":"2021","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025101710111408200_btaf550-B32","doi-asserted-by":"crossref","first-page":"JCS263433","DOI":"10.1242\/jcs.263433","article-title":"The non-canonical Smoothened-AMPK axis regulates Smaug1 biomolecular condensates","volume":"138","author":"Thomas","year":"2025","journal-title":"J. Cell Sci"},{"key":"2025101710111408200_btaf550-B33","doi-asserted-by":"crossref","first-page":"2010","DOI":"10.1093\/bioinformatics\/btac026","article-title":"LLPSDB v2.0: an updated database of proteins undergoing liquid\u2013liquid phase separation in vitro","volume":"38","author":"Wang","year":"2022","journal-title":"Bioinformatics"},{"key":"2025101710111408200_btaf550-B34","doi-asserted-by":"crossref","first-page":"e4756","DOI":"10.1002\/pro.4756","article-title":"ParSe 2.0: a web tool to identify drivers of protein phase separation at the proteome level","volume":"32","author":"Wilson","year":"2023","journal-title":"Protein Sci"},{"key":"2025101710111408200_btaf550-B35","doi-asserted-by":"crossref","first-page":"D354","DOI":"10.1093\/nar\/gkz847","article-title":"PhaSepDB: a database of liquid\u2013liquid phase separation related proteins","volume":"48","author":"You","year":"2020","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf550\/64712643\/btaf550.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/10\/btaf550\/64712643\/btaf550.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/10\/btaf550\/64712643\/btaf550.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T14:11:27Z","timestamp":1760710287000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf550\/8287044"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2025,10]]},"references-count":35,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2025,10,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf550","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,10]]},"published":{"date-parts":[[2025,10]]},"article-number":"btaf550"}}