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Journal Articles Nucleic Acids Research Year : 2023

PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins

Hamidreza Ghafouri
Tamas Lazar
Alessio del Conte
Luiggi G Tenorio Ku
  • Function : Author
Maria Aspromonte
  • Function : Author
Pau Bernadó
  • Function : Author
Belén Chaves-Arquero
  • Function : Author
Lucia Beatriz Chemes
  • Function : Author
Damiano Clementel
  • Function : Author
Tiago Cordeiro
  • Function : Author
Carlos Elena-Real
  • Function : Author
Michael Feig
  • Function : Author
Isabella Felli
  • Function : Author
Carlo Ferrari
  • Function : Author
Julie Forman-Kay
  • Function : Author
Tiago Gomes
  • Function : Author
Frank Gondelaud
  • Function : Author
Claudiu Gradinaru
  • Function : Author
Tâp Ha-Duong
  • Function : Author
Teresa Head-Gordon
  • Function : Author
Pétur Heidarsson
  • Function : Author
Giacomo Janson
  • Function : Author
Gunnar Jeschke
  • Function : Author
Emanuela Leonardi
  • Function : Author
Zi Hao Liu
  • Function : Author
Sonia Longhi
  • Function : Author
Xamuel Lund
  • Function : Author
Maria Macias
  • Function : Author
Pau Martin-Malpartida
  • Function : Author
Davide Mercadante
  • Function : Author
Assia Mouhand
  • Function : Author
Gabor Nagy
  • Function : Author
María Victoria Nugnes
  • Function : Author
Giulia Pesce
  • Function : Author
Roberta Pierattelli
  • Function : Author
Damiano Piovesan
  • Function : Author
Federica Quaglia
  • Function : Author
Sylvie Ricard-Blum
  • Function : Author
Paul Robustelli
  • Function : Author
Amin Sagar
  • Function : Author
Edoardo Salladini
  • Function : Author
Lucile Sénicourt
  • Function : Author
João Teixeira
  • Function : Author
Thomas Tsangaris
  • Function : Author
Mihaly Varadi
  • Function : Author
Pet Er Tompa
Silvio C E Tosatto
  • Function : Author
  • PersonId : 1092155
Alexander Miguel Monzon

Abstract

Abstract The Protein Ensemble Database (PED) (URL: https://proteinensemble.org) is the primary resource for depositing structural ensembles of intrinsically disordered proteins. This updated version of PED reflects advancements in the field, denoting a continual expansion with a total of 461 entries and 538 ensembles, including those generated without explicit experimental data through novel machine learning (ML) techniques. With this significant increment in the number of ensembles, a few yet-unprecedented new entries entered the database, including those also determined or refined by electron paramagnetic resonance or circular dichroism data. In addition, PED was enriched with several new features, including a novel deposition service, improved user interface, new database cross-referencing options and integration with the 3D-Beacons network—all representing efforts to improve the FAIRness of the database. Foreseeably, PED will keep growing in size and expanding with new types of ensembles generated by accurate and fast ML-based generative models and coarse-grained simulations. Therefore, among future efforts, priority will be given to further develop the database to be compatible with ensembles modeled at a coarse-grained level.
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Dates and versions

hal-04266884 , version 1 (31-10-2023)

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Hamidreza Ghafouri, Tamas Lazar, Alessio del Conte, Luiggi G Tenorio Ku, Maria Aspromonte, et al.. PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins. Nucleic Acids Research, 2023, ⟨10.1093/nar/gkad947⟩. ⟨hal-04266884⟩
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