{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T14:00:03Z","timestamp":1790258403182,"version":"4.1.0"},"reference-count":22,"publisher":"Wiley","issue":"10","license":[{"start":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T00:00:00Z","timestamp":1789430400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T00:00:00Z","timestamp":1789430400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100002923","name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Protein Science"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Membraneless organelles formed through liquid\u2013liquid phase separation (LLPS) are fundamental to cellular organization and are involved in multiple processes, including responses to stimuli and stress. The study of disease\u2010associated variants in LLPS proteins remains vital for understanding protein dysfunction in human diseases. However, maintaining specialized, integrative resources is often hindered when database updates rely on human intervention, typically resulting in long intervals between updates. Here, we introduce a major update to DisPhaseDB (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/disphasedb.leloir.org.ar\/\">https:\/\/disphasedb.leloir.org.ar\/<\/jats:ext-link>\n                    ), a comprehensive resource for disease\u2010associated variants in LLPS proteins, integrated with an open\u2010source Snakemake workflow organizing systematic data acquisition and parsing into traceable steps. Crucially, the automated system continuously fetches data from source databases, keeping DisPhaseDB up\u2010to\u2010date without the delays of manual maintenance. The updated release expands the database with additional proteins, increases disease annotation coverage by 174%, and adds clinical significance and allele frequency annotations to enhance variant interpretation. To improve accessibility, we also introduce a Model Context Protocol (MCP) server that establishes a standardized interoperability layer, enabling AI agents and large language models to directly query database records through structured operations. This architecture grounds generative workflows in a trusted source, replacing unconstrained web retrieval and reducing unsupported content. In a comparative benchmark, data retrieval through the MCP server achieved a mean F1 score of 0.99, compared to 0.30 for unguided generative retrieval. Together, these developments position DisPhaseDB2.0 as a maintainable resource for LLPS\u2010related variants, optimizing reproducible data access for both human researchers and emerging agentic AI workflows.\n                  <\/jats:p>","DOI":"10.1002\/pro.70786","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T10:53:06Z","timestamp":1789469586000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["<scp>DisPhaseDB<\/scp>\n                    2.0: Improved interpretation of disease\u2010associated variants in liquid\u2013liquid phase separation proteins with agent\u2010accessible querying"],"prefix":"10.1002","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-8540-3680","authenticated-orcid":false,"given":"Justo","family":"Garcia\u2010Messina","sequence":"first","affiliation":[{"name":"Bioinformatics Unit Fundaci\u00f3n Instituto Leloir\u2010IIBBA\u2010CONICET  Ciudad Aut\u00f3noma de Buenos Aires Argentina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4500-8386","authenticated-orcid":false,"given":"Alvaro M.","family":"Navarro","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit Fundaci\u00f3n Instituto Leloir\u2010IIBBA\u2010CONICET  Ciudad Aut\u00f3noma de Buenos Aires Argentina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6564-1920","authenticated-orcid":false,"given":"Cristina","family":"Marino\u2010Buslje","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit Fundaci\u00f3n Instituto Leloir\u2010IIBBA\u2010CONICET  Ciudad Aut\u00f3noma de Buenos Aires Argentina"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,15]]},"reference":[{"key":"e_1_2_9_2_1","unstructured":"Anthropic.Introducing the Model Context Protocol.2024. Available at:https:\/\/www.anthropic.com\/news\/model-context-protocol."},{"key":"e_1_2_9_3_1","unstructured":"BioContextAI.BioContextAI\u2014Biomedical Model Context Protocol for Agentic AI.2025(cited 2026 May 29). Available at:https:\/\/biocontext.ai."},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06045-0"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34435-x"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12943-025-02428-1"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-025-02900-9"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz972"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41392-024-02013-w"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbaf357"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.59717\/j.xinn-med.2023.100012"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa913"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.29032.1"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2022.05.004"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4858"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2021.06.042"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2025.113843"},{"key":"e_1_2_9_18_1","doi-asserted-by":"crossref","unstructured":"RayPP.A Survey on Model Context Protocol: Architecture State\u2010of\u2010the\u2010art Challenges and Future Directions.2025.","DOI":"10.36227\/techrxiv.174495492.22752319\/v1"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad986"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae1010"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41392-021-00678-1"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2020.09.014"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2020.06.033"}],"container-title":["Protein Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pro.70786","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/pro.70786","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pro.70786","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T13:08:18Z","timestamp":1790255298000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/pro.70786"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,15]]},"references-count":22,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2026,10]]}},"alternative-id":["10.1002\/pro.70786"],"URL":"https:\/\/doi.org\/10.1002\/pro.70786","archive":["Portico"],"relation":{},"ISSN":["0961-8368","1469-896X"],"issn-type":[{"value":"0961-8368","type":"print"},{"value":"1469-896X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,15]]},"assertion":[{"value":"2026-06-23","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-08-17","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-15","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70786"}}