PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.
Lazar, T., Martinez-Perez, E., Quaglia, F., Hatos, A., Chemes, L. B., Iserte, J. A., Mendez, N. A., Garrone, N. A., Saldano, T. E., Marchetti, J., Rueda, A. J. V., Bernado, P., Blackledge, M., Cordeiro, T. N., Fagerberg, E., Forman-Kay, J. D., Fornasari, M. S., Gibson, T. J., Gomes, G. 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., Skepo, M., Svergun, D., Vallet, S. D., Varadi, M., Tompa, P., Tosatto, S. C. E. and Piovesan, D.
VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology, Brussels 1050, Belgium.
Structural Biology Brussels, Bioengineering Sciences Department, Vrije Universiteit Brussel, Brussels 1050, Belgium.
Bioinformatics Unit, Fundacion Instituto Leloir, Buenos Aires, C1405BWE, Argentina.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
Dept. of Biomedical Sciences, University of Padua, Padova 35131, Italy.
Instituto de Investigaciones Biotecnologicas "Dr. Rodolfo A. Ugalde'', IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de SanMartin, CP1650 San Martin, Buenos Aires, Argentina.
Laboratorio de Quimica y Biologia Computacional, Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina.
Centre de Biochimie Structurale (CBS), CNRS, INSERM, University of Montpellier, Montpellier 34090, France.
Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, F-38000, France.
Instituto de Tecnologia Quimica e Biologica Antonio Xavier, Universidade Nova de Lisboa, Av. da Republica, Oeiras 2780-157, Portugal.
Theoretical Chemistry, Lund University, Lund, POB 124, SE-221 00, Sweden.
Molecular Medicine Program, Hospital for Sick Children, Toronto, M5G 1X8, Ontario, Canada.
Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Ontario, Canada.
Department of Physics, University of Toronto, Toronto, M5S 1A7, Ontario, Canada.
Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, L5L 1C6, Ontario, Canada.
Departments of Chemistry, Bioengineering, Chemical and Biomolecular Engineering University of California, Berkeley, CA 94720, USA.
Biocentre, Johannes Gutenberg-University Mainz, Mainz 55128, Germany.
Institute of Molecular Biology, Mainz 55128, Germany.
Aix-Marseille University, CNRS, Architecture et Fonction des Macromolecules Biologiques (AFMB), Marseille 13288, France.
Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
Department of Biomedical Engineering, Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, MO 63130, USA.
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.
LINXS - Lund Institute of Advanced Neutron and X-ray Science, Lund 223 70, Sweden.
European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22607, Germany.
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary.
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.
Nucleic Acids Research 49(D1): D404-D411 (2021)