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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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Cites
Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320
UniProt: a worldwide hub of protein knowledge
The UniProt Consortium (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1049 · Cited by 7,698
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmüller, H., & MacKerell, A. D. (2016) · Nature Methods · doi:10.1038/nmeth.4067 · Cited by 7,334
MolProbity: More and better reference data for improved all‐atom structure validation
Williams, C. J., Headd, J. J., Moriarty, N. W., Prisant, M. G., Videau, L. L., Deis, L. N., Verma, V., Keedy, D. A., Hintze, B. J., Chen, V. B., et al. (2018) · Protein Science · doi:10.1002/pro.3330 · Cited by 4,599
Intrinsically Disordered Proteins in Human Diseases: Introducing the D 2 Concept
Uversky, V. N., Oldfield, C. J., & Dunker, A. K. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.032807.125924 · Cited by 1,447
InterPro in 2019: improving coverage, classification and access to protein sequence annotations
Mitchell, A. L., Attwood, T. K., Babbitt, P. C., Blum, M., Bork, P., Bridge, A., Brown, S. D., Chang, H.-Y., El-Gebali, S., Fraser, M. I., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1100 · Cited by 1,426
Self-citationPolymer physics of intracellular phase transitions
Brangwynne, C., Tompa, P., & Pappu, R. (2015) · Nature Physics · doi:10.1038/nphys3532 · Cited by 1,415
Self-citationA series of PDB related databases for everyday needs
Joosten, R. P., Beek, T. A. H. T., Krieger, E., Hekkelman, M. L., Hooft, R. W. W., Schneider, R., Sander, C., & Vriend, G. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1105 · Cited by 1,313
Structural Characterization of Flexible Proteins Using Small-Angle X-ray Scattering
Bernadó, P., Mylonas, E., Petoukhov, M. V., Blackledge, M. J., & Svergun, D. I. (2007) · Journal of the American Chemical Society · doi:10.1021/ja069124n · Cited by 1,172
Self-citationProtein Data Bank: the single global archive for 3D macromolecular structure data
wwPDB consortium, Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Costanzo, L. D., Christie, C., Duarte, J. M., Dutta, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky949 · Cited by 1,163
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Quaglia, F., Lázár, T., Hatos, A., Tompa, P., Piovesan, D., & Tosatto, S. C. E. (2021) · Current Protocols · doi:10.1002/cpz1.192 · Cited by 5
Self-citationMészáros, A., Ahmed, J., Russo, G., Tompa, P., & Lázár, T. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.1019803 · Cited by 7
Self-citationCehlár, O., Bagarova, O., Hornakova, L., & Škrabana, R. (2021) · General Physiology and Biophysics · doi:10.4149/gpb_2021031 · Cited by 7
Nappi, F. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms262210825 · Cited by 4
Data-driven probabilistic definition of the low energy conformational states of protein residues
Gavaldá-García, J., Bickel, D., Roca‐Martínez, J., Raimondi, D., Orlando, G., & Vranken, W. (2024) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqae082 · Cited by 4
Description of conformational ensembles of disordered proteins by residue-local probabilities
Bastida, A., Zúñiga, J., Miguel, B., & Soler, M. A. (2023) · Physical Chemistry Chemical Physics · doi:10.1039/d2cp05970c · Cited by 3
Why are there no clinically-approved drugs targeting disordered proteins?
Löhr, T., Karunanithy, G., & Heller, G. T. (2026) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2026.103236 · Cited by 4
Wohl, S., Gilron, Y., & Zheng, W. (2025) · ACS Physical Chemistry Au · doi:10.1021/acsphyschemau.5c00005 · Cited by 5
Can sequence-specific and dynamics-based metrics allow us to decipher the function in IDP sequences?
Ozkan, S. B. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.04.008 · Cited by 3
Hornakova, L., Šinský, J., Janubova, M., Mederlyova, A., Ivanovova, N. P., Piešťanský, J., Kováč, A., Galba, J., Škrabana, R., & Cehlár, O. (2022) · FEBS Letters · doi:10.1002/1873-3468.14339 · Cited by 3
Ammar, A., Mičetić, I., & Gray, A. J. G. (2022) · doi:10.37044/osf.io/7f95d · Cited by 3
Gu, Z.-Q., Wang, H.-T., Li, Y., Krogsaeter, E., Lin, A. C., Lin, J., Liu, Y.-S., Lin, W., Burton, W., Liu, M.-L., et al. (2025) · Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · doi:10.1016/j.biopha.2025.118350 · Cited by 4
Prediction of protein structure and intrinsic disorder in the era of deep learning
Erdős, G., & Dosztányi, Z. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-99533-7.00007-8 · Cited by 2
Im, J., Lee, K., Jung, S., Kim, E., & Lee, J. H. (2021) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.1c02605 · Cited by 2
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Coskuner‐Weber, O., & Uversky, V. N. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-21809-5.00015-6 · Cited by 1
Vu, Q. V., Sitarik, I. M., Li, M. S., & O’Brien, E. P. (2025) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5c01260 · Cited by 1
Tahzima, R., Charon, J., Díaz, A., Jonghe, K. D., Massart, S., Michon, T., & Vranken, W. (2025) · Frontiers in Virology · doi:10.3389/fviro.2025.1501616 · Cited by 1
Topological Investigation of Protein Folding and Intrinsic Disorder
Hammond, M. E., Akulov, V., van Noort, J., Zwep, L. B., & Mashaghi, A. (2026) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5c08075 · Cited by 1
In search of shape in the unshaped: Constructing ensembles of intrinsically disordered proteins
Saha, D., Yang, W., & Zheng, W. (2026) · Biophysics Reviews · doi:10.1063/5.0307183 · Cited by 1
Liu, W., Tian, L., Xie, J., Wu, L., Hu, L., Ge, R., Wang, Y., & Cao, M. (2026) · Biotechnology Advances · doi:10.1016/j.biotechadv.2026.108931 · Cited by 1
Intrinsically disordered proteins: functionality of chaos
Singh, A., Maji, T., Banerjee, P., & De, S. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-21809-5.00019-3 · Cited by 1
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Tsangaris, T. E., Smyth, S., Gomes, G.-N. W., Liu, Z.-H., Milchberg, M. H., Bah, A., Wasney, G., Forman-Kay, J., & Gradinaru, C. (2023) · bioRxiv · doi:10.1101/2023.06.20.545775 · Cited by 7
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Bolding, J. E., Nielsen, A. L., Jensen, I., Hansen, T. N., Ryberg, L. A., Jameson, S. T., Harris, P., Peters, G. H. J., Denu, J. M., Rogers, J. M., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.16.545261
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Shi, J., Wang, R., Rebello, N., Lu, J., Olsen, B. D., & Audus, D. J. (2026) · Macromolecules · doi:10.1021/acs.macromol.5c03015
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Zela, C. I., Castellar, C., Franco, D. D. O., Júnior, A. L. G., Calegario, R. F., & Mio, L. L. M. D. (2026) · Brazilian Journal of Microbiology · doi:10.1007/s42770-026-01967-z
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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
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