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Cited by 143Protein Structure and DynamicsEnzyme Structure and FunctionComputational Drug Discovery Methods

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PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins

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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·2021·Nucleic Acids Research
DOI 10.1093/nar/gkaa1021PMC PMC7778965
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Abstract

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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Crossref · 10.1093/nar/gkaa1021

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Figures

Figure 1. PED 4.0 entry statistics. Stacked histogram of models per ensemble for different measurement methods in PED 4.0, binned based on the number of the consisting conformer models.
Figure 1. PED 4.0 entry statistics. Stacked histogram of models per ensemble for different measurement methods in PED 4.0, binned based on the number of the consisting conformer models.CC BY-NC · PubMed Central
Figure 2. Chain compactness of PED 4.0 entries. Radius of gyration of protein chains plotted against their chain length. Each dot represents a given chain in a given ensemble. The reference curves (54) represent values specific for folded proteins (purple), random coils (blue), denatured proteins (green) and fully extended chains (red). Four long folded proteins (PED00007, PED00010, PED00014 and PED00162) with over 300 residues are omitted, but fit well to the purple trend line.
Figure 2. Chain compactness of PED 4.0 entries. Radius of gyration of protein chains plotted against their chain length. Each dot represents a given chain in a given ensemble. The reference curves (54) represent values specific for folded proteins (purple), random coils (blue), denatured proteins (green) and fully extended chains (red). Four long folded proteins (PED00007, PED00010, PED00014 and PED00162) with over 300 residues are omitted, but fit well to the purple trend line.CC BY-NC · PubMed Central
Figure 3. Example for PED’s Protein page. Protein page P04637 summarizes the human p53 ensembles currently stored in PED for both the N-terminal and C-terminal disordered region. The feature viewer also integrates intrinsic disorder evidence from DisProt.
Figure 3. Example for PED’s Protein page. Protein page P04637 summarizes the human p53 ensembles currently stored in PED for both the N-terminal and C-terminal disordered region. The feature viewer also integrates intrinsic disorder evidence from DisProt.CC BY-NC · PubMed Central
Figure 4. Example for PED’s Entry page. Entry page is shown for the C-terminal disordered region of p53 in a tetrameric complex with Ca2+-bound S100B (PED00063). The feature viewer shows chain-specific information, while molecular graphics, Ramachandran maps and Rg distribution are presented below.
Figure 4. Example for PED’s Entry page. Entry page is shown for the C-terminal disordered region of p53 in a tetrameric complex with Ca2+-bound S100B (PED00063). The feature viewer shows chain-specific information, while molecular graphics, Ramachandran maps and Rg distribution are presented below.CC BY-NC · PubMed Central

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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
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
DOI
10.1093/nar/gkaa1021
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
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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