{ "abstract": "The Protein Ensemble Database (PED; https://proteinensemble.org) is the primary deposition resource for structural ensembles of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs). PED 2027 (released in September 2026) substantially expands its scope by integrating ensembles determined or refined using experimental data with clearly identified collections of computational predictions. The release introduces a multi-method collection targeting 3319 DisProt proteins and 2452 manually curated disordered regions, together with AlphaFlex ensembles for 10 022 human proteins containing IDRs. Alternative predictions for the same sequence are retained as independent records with method-specific provenance, enabling comparison across ensemble-generation approaches. A scalable deposition workflow accommodates individual experimental studies and proteome-scale collections while preserving quality control and curator oversight. The PED controlled vocabulary standardizes experimental data acquisition, computational generation, selection, and refinement. Precomputed IDPEnsembleTools and CIDER analyses provide structural and sequence-derived descriptors directly on ensemble pages. A redesigned interface and extended REST API support discovery, visualization, download and programmatic access. Interoperability with UniProt, DisProt, MobiDB, and experimental-data repositories connects ensembles with sequences, annotations, and supporting measurements. PED 2027 therefore provides an interoperable, analysis-ready platform for studying IDP/IDR conformational behaviour.", "abstract_shown": true, "affiliations": [ "Department of Biomedical Sciences, University of Padova , 35131 Padova ,", "Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200Copenhagen ,", "Department of Chemistry, University of Massachusetts , Amherst, MA 01003 ,", "Centre de Biologie Structurale (CBS), University of Montpellier, INSERM, CNRS , 34090", "Institut Pasteur, Université Paris Cité, CNRS UMR3528, Computational Structural Biology Unit , F-75015 Paris ,", "Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Avenida da República, 2780-157 Oeiras ,", "Université de Toulouse, CNRS, LAAS , 31400Toulouse ,", "Pitzer Theory Center and Department of Chemistry, University of California , Berkeley, CA 94720 ,", "Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, MO 63110 ,", "Center for Biomolecular Condensates, Washington University in St. Louis , St. Louis, MO ,", "Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, MI48824 ,", "Molecular Medicine Program, The Hospital for Sick Children , M5G 1X8Toronto, Ontario ,", "Department of Biochemistry, University of Toronto , M5S 1A8Toronto, Ontario ,", "Pitzer Theory Center and Departments of Chemistry, Bioengineering, and Chemical and Biomolecular Engineering, University of California , Berkeley, CA 94720 ,", "Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix-Marseille Université and CNRS , 13288Marseille ,", "CNRS, LAAS , 31400Toulouse ,", "Department of Chemistry, Dartmouth College , Hanover, NH 03755 ,", "University of Montpellier, CNRS , 34090Montpellier ,", "Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge , Cambridge CB2 1EW ," ], "article_type": null, "arxiv": null, "author_total": 29, "authors": [ { "affs": [ 0 ], "name": "Alexander Miguel Monzon", "orcid": "0000-0003-0362-8218" }, { "affs": [ 1 ], "name": "Hamidreza Ghafouri" }, { "affs": [ 0 ], "name": "Ximena Aixa Castro" }, { "affs": [ 0 ], "name": "Sina Khezrian", "orcid": "0009-0002-8418-649X" }, { "affs": [ 0 ], "name": "Maria Cristina Aspromonte", "orcid": "0000-0002-4937-6952" }, { "affs": [ 0 ], "name": "Kavita Singla" }, { "affs": [ 2 ], "name": "Shrishti Barethiya" }, { "affs": [ 3 ], "name": "Pau Bernadó", "orcid": "0000-0001-7395-5922" }, { "affs": [ 4 ], "name": "Massimiliano Bonomi" }, { "affs": [ 2 ], "name": "Jianhan Chen", "orcid": "0000-0002-5281-1150" }, { "affs": [ 5 ], "name": "Tiago Cordeiro" }, { "affs": [ 6 ], "name": "Juan Cortés", "orcid": "0000-0002-4660-0306" }, { "affs": [ 7 ], "name": "Stefano De Castro" }, { "affs": [ 8, 9 ], "name": "Ryan Emenecker", "orcid": "0000-0001-7055-2773" }, { "affs": [ 10 ], "name": "Michael Feig" }, { "affs": [ 11, 12 ], "name": "Julie D Forman-Kay" }, { "affs": [ 13 ], "name": "Teresa Head-Gordon", "orcid": "0000-0003-0025-8987" }, { "affs": [ 8, 9 ], "name": "Alex Holehouse", "orcid": "0000-0002-4155-5729" }, { "affs": [ 10 ], "name": "Giacomo Janson" }, { "affs": [ 1 ], "name": "Kresten Lindorff-Larsen", "orcid": "0000-0002-4750-6039" }, { "affs": [ 11, 12 ], "name": "Zi Hao Liu", "orcid": "0000-0002-8357-8507" }, { "affs": [ 14 ], "name": "Sonia Longhi" }, { "affs": [ 15 ], "name": "Matyas Pajkos" }, { "affs": [ 16 ], "name": "Paul Robustelli" }, { "affs": [ 3 ], "name": "Santiago Rodriguez" }, { "affs": [ 4 ], "name": "Vincent Schnapka", "orcid": "0000-0002-3902-5462" }, { "affs": [ 17 ], "name": "Nathalie Sibille", "orcid": "0000-0001-8145-6795" }, { "affs": [ 18 ], "name": "Michele Vendruscolo", "orcid": "0000-0002-3616-1610" }, { "affs": [ 0 ], "name": "Silvio C E Tosatto", "orcid": "0000-0003-4525-7793" } ], "bibtex": "https://research.draconitic.com/paper/fkb0kh4f9ewhe.bib", "cited_by": 0, "doi": "10.1093/nar/gkag1048", "fulltext_url": null, "id": "fkb0kh4f9ewhe", "issns": [ "0305-1048", "1362-4962" ], "landing_url": "https://hal.science/hal-05843399v1", "language": "en", "licence": "CC-BY-NC-4.0", "licence_label": "CC BY-NC 4.0", "licence_source": "article", "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/", "metadata_licence": null, "native_subjects": [ [ "hal", "0.sdv" ], [ "openalex", "1312|Protein Structure and Dynamics" ] ], "openalex": "W7223894013", "pdf_url": "https://hal.science/hal-05843399/document", "pmcid": null, "pmid": "42934172", "published": "2026-10-27", "publisher": "Oxford University Press", "ris": "https://research.draconitic.com/paper/fkb0kh4f9ewhe.ris", "sources": [ { "first_seen": "2026-10-30T12:18:03Z", "native_id": "hal-05843399", "source": "hal", "url": "https://hal.science/hal-05843399v1" }, { "first_seen": "2026-10-30T12:18:50Z", "native_id": "10.1093/nar/gkag1048", "source": "crossref", "url": "https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1048/9002499" } ], "subjects": [ { "field": "biochemistry", "origin": "openalex:1312|Protein Structure and Dynamics", "subfield": "molecular-biology" } ], "title": "PED in 2027: integrating experimental and predicted protein conformational ensembles at scale", "title_text": "PED in 2027: integrating experimental and predicted protein conformational ensembles at scale", "type": "peer-reviewed", "updated_at": "2026-10-31T12:20:56Z", "url": "https://research.draconitic.com/paper/fkb0kh4f9ewhe", "venue": "Nucleic Acids Research", "versions": [] }