PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins-Reference-Cited by-同舟云学术

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

Published:2020-12-10 Issue:D1 Volume:49 Page:D404-D411
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Lazar Tamas¹²^ORCID,Martínez-Pérez Elizabeth³⁴^ORCID,Quaglia Federica⁵^ORCID,Hatos András⁵^ORCID,Chemes Lucía B⁶^ORCID,Iserte Javier A³^ORCID,Méndez Nicolás A⁶^ORCID,Garrone Nicolás A⁶^ORCID,Saldaño Tadeo E⁷^ORCID,Marchetti Julia⁷^ORCID,Rueda Ana Julia Velez⁷^ORCID,Bernadó Pau⁸^ORCID,Blackledge Martin⁹^ORCID,Cordeiro Tiago N⁸¹⁰^ORCID,Fagerberg Eric¹¹^ORCID,Forman-Kay Julie D¹²¹³^ORCID,Fornasari Maria S⁷^ORCID,Gibson Toby J⁴^ORCID,Gomes Gregory-Neal W¹⁴¹⁵^ORCID,Gradinaru Claudiu C¹⁴¹⁵^ORCID,Head-Gordon Teresa¹⁶^ORCID,Jensen Malene Ringkjøbing⁹^ORCID,Lemke Edward A¹⁷¹⁸^ORCID,Longhi Sonia¹⁹^ORCID,Marino-Buslje Cristina³^ORCID,Minervini Giovanni⁵^ORCID,Mittag Tanja²⁰^ORCID,Monzon Alexander Miguel⁵^ORCID,Pappu Rohit V²¹^ORCID,Parisi Gustavo⁷^ORCID,Ricard-Blum Sylvie²²^ORCID,Ruff Kiersten M²¹,Salladini Edoardo¹⁹^ORCID,Skepö Marie¹¹²³^ORCID,Svergun Dmitri²⁴^ORCID,Vallet Sylvain D²²^ORCID,Varadi Mihaly²⁵^ORCID,Tompa Peter¹²²⁶^ORCID,Tosatto Silvio C E⁵^ORCID,Piovesan Damiano⁵^ORCID

Affiliation:

1. VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology, Brussels 1050, Belgium

2. Structural Biology Brussels, Bioengineering Sciences Department, Vrije Universiteit Brussel, Brussels 1050, Belgium

3. Bioinformatics Unit, Fundación Instituto Leloir, Buenos Aires, C1405BWE, Argentina

4. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany

5. Dept. of Biomedical Sciences, University of Padua, Padova 35131, Italy

6. Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde’’, IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de SanMartín, CP1650 San Martín, Buenos Aires, Argentina

7. Laboratorio de Química y Biología Computacional, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina

8. Centre de Biochimie Structurale (CBS), CNRS, INSERM, University of Montpellier, Montpellier 34090, France

9. Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, F-38000, France

10. Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal

11. Theoretical Chemistry, Lund University, Lund, POB 124, SE-221 00, Sweden

12. Molecular Medicine Program, Hospital for Sick Children, Toronto, M5G 1X8, Ontario, Canada

13. Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Ontario, Canada

14. Department of Physics, University of Toronto, Toronto, M5S 1A7, Ontario, Canada

15. Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, L5L 1C6, Ontario, Canada

16. Departments of Chemistry, Bioengineering, Chemical and Biomolecular Engineering University of California, Berkeley, CA 94720, USA

17. Biocentre, Johannes Gutenberg-University Mainz, Mainz 55128, Germany

18. Institute of Molecular Biology, Mainz 55128, Germany

19. Aix-Marseille University, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille 13288, France

20. Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA

21. Department of Biomedical Engineering, Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, MO 63130, USA

22. 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

23. LINXS - Lund Institute of Advanced Neutron and X-ray Science, Lund 223 70, Sweden

24. European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22607, Germany

25. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK

26. Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary

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.

Funder

Italian Ministry of University and Research

Horizon 2020

Hungarian Scientific Research Fund

Universidad Nacional de Quilmes

National Agency for the Promotion of Science and Technology

LBC

Fondation pour la Recherche Médicale

Natural Sciences and Engineering Research Council of Canada

Agence Nationale de la Recherche

National Institutes of Health

German Ministry of Science and Education