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PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins
Open accessAbstract
The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs.
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Metadata
- Authors
- Lazar, T., Martínez-Pérez, E., Quaglia, F., Hatos, A., Chemes, L. B., Iserte, J. A., Méndez, N. A., Garrone, N. A., Saldaño, T. E., Marchetti, J., Rueda, A. J. V., Bernadó, P., Blackledge, M., Cordeiro, T. N., Fagerberg, E., Forman-Kay, J. D., Fornasari, M. S., Gibson, T. J., Gomes, G.-N. W., Gradinaru, C. C., Head-Gordon, T., Jensen, M. R., Lemke, E. A., Longhi, S., Marino-Buslje, C., Minervini, G., Mittag, T., Monzon, A. M., Pappu, R. V., Parisi, G., Ricard-Blum, S., Ruff, K. M., Salladini, E., Skepö, M., Svergun, D., Vallet, S. D., Varadi, M., Tompa, P., Tosatto, S. C. E., & Piovesan, D.
- Affiliations
- VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology, Brussels 1050, Belgium
- Bioinformatics Unit, Fundación Instituto Leloir, Buenos Aires, C1405BWE, Argentina
- University of Padua (IT)
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde’’, IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de SanMartín, CP1650 San Martín, Buenos Aires, Argentina
- Fundación Instituto Leloir (AR)
- Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
- National University of Quilmes (AR)
- Centre National de la Recherche Scientifique (FR)
- Lund University (SE)
- University of Toronto (CA)
- Laboratorio de Química y Biología Computacional, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina
- European Molecular Biology Laboratory (DE)
- University of California, Berkeley (US)
- Johannes Gutenberg University Mainz (DE)
- St. Jude Children's Research Hospital (US)
- Dept. of Biomedical Sciences, University of Padua, Padova 35131, Italy
- Washington University in St. Louis (US)
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, Villeurbanne, 69629 Lyon Cedex 07, France
- Lyon 1 Université (FR)
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
- Corresponding author
- Tosatto, Silvio C E
- ORCID
- Lazar, Tamas
- Martínez-Pérez, Elizabeth
- Quaglia, Federica
- Hatos, András
- Chemes, Lucía B
- Iserte, Javier A
- Méndez, Nicolás A
- Garrone, Nicolás A
- Saldaño, Tadeo E
- Marchetti, Julia
- Rueda, Ana Julia Velez
- Bernadó, Pau
- Blackledge, Martin
- Cordeiro, Tiago N
- Fagerberg, Eric
- Forman-Kay, Julie D
- Fornasari, Maria S
- Gibson, Toby J
- Gomes, Gregory-Neal W
- Gradinaru, Claudiu C
- Head-Gordon, Teresa
- Jensen, Malene Ringkjøbing
- Lemke, Edward A
- Longhi, Sonia
- Marino-Buslje, Cristina
- Minervini, Giovanni
- Mittag, Tanja
- Monzon, Alexander Miguel
- Pappu, Rohit V
- Parisi, Gustavo
- Ricard-Blum, Sylvie
- Ruff, Kiersten M
- Salladini, Edoardo
- Skepö, Marie
- Svergun, Dmitri
- Vallet, Sylvain D
- Varadi, Mihaly
- Tompa, Peter
- Tosatto, Silvio C E
- Piovesan, Damiano
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-12-10
- Volume
- 49
- Issue
- D1
- Pages
- D404-D411
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC7778965
- OpenAlex
- W3112873140
- Cited by
- 142
- References
- 65
- Citations by year
- 2026: 12 · 2025: 18 · 2024: 20 · 2023: 35 · 2022: 34 · 2021: 20 · 2020: 3
- FWCI
- 7.54
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HAL AMU (submittedVersion, other-oa)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion, other-oa)
- HAL (submittedVersion)
- HAL (submittedVersion, cc-by-nc)
- eScholarship (California Digital Library) (submittedVersion)
- Lund University Publications (Lund University) (submittedVersion, cc-by-nc)
- Conicet (submittedVersion, cc-by-nc)
- VUBIR (Vrije Universiteit Brussel) (submittedVersion)
- Padua Research Archive (University of Padova) (submittedVersion)
- Padua Research Archive (University of Padova) (submittedVersion, cc-by-nc)
- Funders
- Italian Ministry of University and Research (2017483NH8)
- Horizon 2020 (778247, 871037)
- Hungarian Scientific Research Fund (K124670, K131702)
- Universidad Nacional de Quilmes (PUNQ 1309/19)
- National Agency for the Promotion of Science and Technology (PICT-2014-3430)
- LBC (PICT-2017-1924)
- Fondation pour la Recherche Médicale (DBI20141231336)
- Natural Sciences and Engineering Research Council of Canada (RGPIN 2017-0603)
- Agence Nationale de la Recherche (ANR-10-LABX-12-01)
- National Institutes of Health (5R01GM127627-03)
- German Ministry of Science and Education (16QK10A)
- Vrije Universiteit Brussel (SRP51)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Keywords
- intrinsically disordered proteins, structural ensembles, database redesign, biocuration, metadata, search engines, DisProt
- MeSH terms
- Humans, Tumor Suppressor Protein p53, Databases, Protein, Search Engine, Intrinsically Disordered Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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