PED in 2021 : A major update of the protein ensemble database for intrinsically disordered proteins
(2021) In Nucleic Acids Research 49(D1). p.404-411- 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... (More)
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.
(Less)
- author
- organization
- publishing date
- 2021-01-08
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Nucleic Acids Research
- volume
- 49
- issue
- D1
- pages
- 8 pages
- publisher
- Oxford University Press
- external identifiers
-
- scopus:85095859724
- pmid:33305318
- ISSN
- 0305-1048
- DOI
- 10.1093/nar/gkaa1021
- language
- English
- LU publication?
- yes
- additional info
- Funding Information: PED is maintained as a service of the ELIXIR IDP community (URL: elixir-europe.org/communities/intrinsicallydisordered-proteins). This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 778247. Italian Ministry of University and Research (MIUR) to SCET [2017483NH8]; European Union's Horizon 2020 to SCET [778247]; Hungarian Scientific Research Fund (OTKA) to PT [K124670, K131702]; Universidad Nacional de Quilmes to GP [PUNQ 1309/19]; National Agency for the Promotion of Science and Technology (ANPCyT) to GP [PICT-2014-3430] and to LBC [PICT-2017-1924]; Fondation pour la Recherche M?dicale to SRB and SDV [DBI20141231336]; Natural Sciences and Engineering Research Council of Canada to CCG [RGPIN 2017-06030]; Agence Nationale de la Recherche (ANR) to PB [ANR-10-LABX-12-01]; National Institutes of Health (NIH) to JFK and THG [5R01GM127627-03]; German Ministry of Science and Education (SAS-BSOFT) to DS [16QK10A]; EU Horizon 2020 programme (iNEXT-Discovery) to DS [871037]; Vrije Universiteit Brussel (VUB) to PT [SRP51]; EM-P, NG, NM, JM are PhD students, AJVR, TES are Postdocs and GP, CM-B, JI, LBC and MSF are researchers of the National Research Council (CONICET) of Argentina. Funding for open access charge: Vrije Universiteit Brussel (VUB) [SRP51]. Publisher Copyright: © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
- id
- 0790a52f-a49a-4ce1-8689-4191f21881f2
- alternative location
- https://academic.oup.com/nar/article-abstract/49/D1/D404/6030232
- date added to LUP
- 2021-10-12 21:56:12
- date last changed
- 2024-06-01 17:18:10
@article{0790a52f-a49a-4ce1-8689-4191f21881f2,
abstract = {{<p>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.</p>}},
author = {{Lazar, Tamas and Martínez-Pérez, Elizabeth and Quaglia, Federica and Hatos, András and Chemes, Lucía B. and Iserte, Javier A. and Méndez, Nicolás A. and Garrone, Nicolás A. and Saldaño, Tadeo E. and Marchetti, Julia and Rueda, Ana Julia Velez and Bernadó, Pau and Blackledge, Martin and Cordeiro, Tiago N. and Fagerberg, Eric and Forman-Kay, Julie D. and Fornasari, Maria S. and Gibson, Toby J. and Gomes, Gregory Neal W. and Gradinaru, Claudiu C. and Head-Gordon, Teresa and Jensen, Malene Ringkjøbing and Lemke, Edward A. and Longhi, Sonia and Marino-Buslje, Cristina and Minervini, Giovanni and Mittag, Tanja and Monzon, Alexander Miguel and Pappu, Rohit V. and Parisi, Gustavo and Ricard-Blum, Sylvie and Ruff, Kiersten M. and Salladini, Edoardo and Skepö, Marie and Svergun, Dmitri and Vallet, Sylvain D. and Varadi, Mihaly and Tompa, Peter and Tosatto, Silvio C.E. and Piovesan, Damiano}},
issn = {{0305-1048}},
language = {{eng}},
month = {{01}},
number = {{D1}},
pages = {{404--411}},
publisher = {{Oxford University Press}},
series = {{Nucleic Acids Research}},
title = {{PED in 2021 : A major update of the protein ensemble database for intrinsically disordered proteins}},
url = {{http://dx.doi.org/10.1093/nar/gkaa1021}},
doi = {{10.1093/nar/gkaa1021}},
volume = {{49}},
year = {{2021}},
}