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IDRs are critical for biological regulation and organization, as targets for post-translational modifications, and as mediators of biomolecular condensates. To address the pressing need for better structural models enabling functional insight, we developed AlphaFlex to model fully atomistic conformer ensembles for proteins predicted to have IDRs, modeled in the context of AlphaFold folded domains and an implicit bilayer for transmembrane proteins. The AlphaFlex resource provides conformational ensembles of human proteins from the AlphaFold database with identified IDRs in the Protein Ensemble Database that is mirrored in UniProt. This transformative resource of AlphaFlex ensembles provides physically and biologically relevant full-length models for IDR proteins, including scaffold proteins, those with IDR:folded-domain interactions, regulatory and condensate proteins requiring exposed binding elements, conditionally folding IDRs, and transmembrane proteins containing IDRs.<\/jats:p>","DOI":"10.1101\/2025.11.24.690279","type":"posted-content","created":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T03:20:18Z","timestamp":1764127218000},"source":"Crossref","is-referenced-by-count":9,"title":["AlphaFlex: Ensembles of the human proteome representing disordered regions"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8357-8507","authenticated-orcid":false,"given":"Zi Hao","family":"Liu","sequence":"first","affiliation":[{"name":"Program in Molecular Medicine, Hospital for Sick Children; Toronto, Canada"},{"name":"Department of Biochemistry, University of Toronto; Toronto, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oufan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California; Berkeley, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-8497-3531","authenticated-orcid":false,"given":"Stefano","family":"De Castro","sequence":"additional","affiliation":[{"name":"Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California; Berkeley, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6472-1665","authenticated-orcid":false,"given":"Kunyang","family":"Sun","sequence":"additional","affiliation":[{"name":"Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California; Berkeley, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-3079-9229","authenticated-orcid":false,"given":"Hamidreza","family":"Ghafouri","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padova; Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-2327-9430","authenticated-orcid":false,"given":"Omar Abdelghani","family":"Attafi","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padova; Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5483-0577","authenticated-orcid":false,"given":"Nicolas L.","family":"Fawzi","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University; Providence, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4525-7793","authenticated-orcid":false,"given":"Silvio C. 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