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Journal Articles Nucleic Acids Research Year : 2021

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

Tamas Lazar
Elizabeth Martínez-Pérez
Lucía Chemes
  • Function : Author
Javier Iserte
Nicolás Méndez
Nicolás Garrone
Tadeo Saldaño
  • Function : Author
Ana Julia Velez Rueda
  • Function : Author
Pau Bernadó
Martin Blackledge
Tiago Cordeiro
Eric Fagerberg
Julie Forman-Kay
Maria Fornasari
  • Function : Author
Toby Gibson
Gregory-Neal Gomes
Claudiu Gradinaru
  • Function : Author
Teresa Head-Gordon
Edward Lemke
  • Function : Author
Sonia Longhi
Cristina Marino-Buslje
Giovanni Minervini
Tanja Mittag
Alexander Miguel Monzon
  • Function : Author
Rohit Pappu
Gustavo Parisi
Sylvie Ricard-Blum
Kiersten Ruff
  • Function : Author
Edoardo Salladini
Marie Skepö
Dmitri Svergun
Sylvain Vallet
  • Function : Author
Mihaly Varadi
Peter Tompa
Silvio Tosatto
Damiano Piovesan

Abstract

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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Dates and versions

hal-03433964 , version 1 (18-11-2021)

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Cite

Tamas Lazar, Elizabeth Martínez-Pérez, Federica Quaglia, András Hatos, Lucía Chemes, et al.. PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins. Nucleic Acids Research, 2021, 49 (D1), pp.D404-D411. ⟨10.1093/nar/gkaa1021⟩. ⟨hal-03433964⟩
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