PED in 2027: integrating experimental and predicted protein conformational ensembles at scale

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.

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Publication Details

Journal
Nucleic Acids Research
Published
2026-10-27
DOI
https://doi.org/10.1093/nar/gkag1048
Primary Topic
Protein Structure and Dynamics
Type
article
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article

PED in 2027: integrating experimental and predicted protein conformational ensembles at scale

Kavita Singla, Pau Bernadó, Kresten Lindorff‐Larsen, Hamidreza Ghafouri et al.
1 links
Nucleic Acids Research
Protein Structure and Dynamics
article

PED in 2027: integrating experimental and predicted protein conformational ensembles at scale

Kavita Singla, Pau Bernadó, Kresten Lindorff‐Larsen, Hamidreza Ghafouri, Jianhan Chen, Maria Cristina Aspromonte, Ryan J. Emenecker, Michele Vendruscolo, Vincent Schnapka, T. Cordeiro, Alex S. Holehouse, Massimiliano Bonomi, Teresa L. Head-Gordon, Alexander Miguel Monzón, Michael Feig, Silvio C. E. Tosatto, Juan Cortés, Sonia Longhi, Giacomo Janson, Mátyás Pajkos, Paul Robustelli, Zi Hao Liu, Julie Deborah Forman-Kay, Shrishti Barethiya, Nathalie Sibille, Ximena Aixa Castro, Santiago Rodriguez, Stefano De Castro, Sina Khezrian
article en

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.

Nucleic Acids Research
Dartmouth College (US), University of Copenhagen (DK), Centre National de la Recherche Scientifique (FR), University of Padua (IT), Pitzer College (US), Inserm (FR), Institut Pasteur (FR), Université Fédérale de Toulouse Midi-Pyrénées (FR), University of Toronto (CA), Université de Montpellier (FR), Washington University in St. Louis (US), Université Paris Cité (FR), Aix-Marseille Université (FR), University of Cambridge (GB), University of Massachusetts Amherst (US), Hospital for Sick Children (CA), Centre de Biologie Structurale (FR), Architecture et Fonction des Macromolécules Biologiques (FR), Biologie Moléculaire Structurale et Processus Infectieux (FR), Université de Toulouse (FR), Instituto de Tecnologia Química e Biológica António Xavier (PT), Universidade Nova de Lisboa (PT), Michigan State University (US), University of California, Berkeley (US)
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Protein Structure and Dynamics
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