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DisProt: intrinsic protein disorder annotation in 2020

Authors :
Hatos, András
Hajdu-Soltész, Borbála
Monzon, Alexander M.
Palopoli, Nicolas
Álvarez, Lucía
Aykac-Fas, Burcu
Bassot, Claudio
Benítez, Guillermo I.
Bevilacqua, Martina
Chasapi, Anastasia
Chemes, Lucia
Davey, Norman E.
Davidović, Radoslav
Dunker, A. Keith
Elofsson, Arne
Gobeill, Julien
Foutel, Nicolás S. González
Sudha, Govindarajan
Guharoy, Mainak
Horvath, Tamas
Iglesias, Valentin
Kajava, Andrey V.
Kovacs, Orsolya P.
Lamb, John
Lambrughi, Matteo
Lazar, Tamas
Leclercq, Jeremy Y.
Leonardi, Emanuela
Macedo-Ribeiro, Sandra
Macossay-Castillo, Mauricio
Maiani, Emiliano
Manso, José A.
Marino-Buslje, Cristina
Martínez-Pérez, Elizabeth
Mészáros, Bálint
Mičetić, Ivan
Minervini, Giovanni
Murvai, Nikoletta
Necci, Marco
Ouzounis, Christos A.
Pajkos, Mátyás
Paladin, Lisanna
Pancsa, Rita
Papaleo, Elena
Parisi, Gustavo
Pasche, Emilie
Barbosa Pereira, Pedro J.
Promponas, Vasilis J.
Pujols, Jordi
Quaglia, Federica
Ruch, Patrick
Salvatore, Marco
Schad, Eva
Szabo, Beata
Szaniszló, Tamás
Tamana, Stella
Tantos, Agnes
Veljkovic, Nevena
Ventura, Salvador
Vranken, Wim
Dosztányi, Zsuzsanna
Tompa, Peter
Tosatto, Silvio C. E.
Piovesan, Damiano
Promponas, Vasilis J. [0000-0003-3352-4831]
Universita degli Studi di Padova
Vinča Institute of Nuclear Sciences
University of Belgrade [Belgrade]
Stockholm University
Laboratoire Leibniz (Leibniz - IMAG)
Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique de Grenoble (INPG)-Université Joseph Fourier - Grenoble 1 (UJF)
Laboratoire de biochimie théorique [Paris] (LBT (UPR_9080))
Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut de biologie physico-chimique (IBPC (FR_550))
Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)
Reproductive Neuroscience Unit, Department of Obstetrics and Gynecology and Department of Neurobiology
Yale University School of Medicine
Centre de recherche en Biologie Cellulaire (CRBM)
Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Università degli Studi di Modena e Reggio Emilia (UNIMORE)
Structural Biology Brussels (SBB)
Vrije Universiteit Brussel (VUB)
Instituto de Biologia Molecular e Celular (IBMC)
Hungarian Academy of Sciences (MTA)
Institute of Agrobiotechnology
National Center for Research and Technology
Universidad Nacional de Quilmes (UNQ)
Université de Genève et Hôpitaux Universitaires de Genève (SIM)
Hôpitaux Universitaires de Genève (HUG)
Biophysics and Bioinformatics Laboratory
Institut de Biotecnologia i Biomedicina
Universitat Autònoma de Barcelona (UAB)
Service d'informatique médicale (SIM)
Hôpitaux de Genève
Department of Structural Biology
Biophysics Research Group [Budapest] (ELTE-MTA 'Lendület')
Department of Bio-engineering Sciences
Structural Biology Brussels
Faculty of Sciences and Bioengineering Sciences
Informatics and Applied Informatics
Chemistry
Basic (bio-) Medical Sciences
Instituto de Investigação e Inovação em Saúde
Université Joseph Fourier - Grenoble 1 (UJF)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)
Université Paris Diderot - Paris 7 (UPD7)-Institut de biologie physico-chimique (IBPC)
Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)
Vrije Universiteit [Brussels] (VUB)
Universitat Autònoma de Barcelona [Barcelona] (UAB)
Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Institut de biologie physico-chimique (IBPC (FR_550))
Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Source :
Nucleic Acids Research, Nucleic Acids Res., Nucleic Acids Research, Oxford University Press, 2019, ⟨10.1093/nar/gkz975⟩, Dipòsit Digital de Documents de la UAB, Universitat Autònoma de Barcelona, Hatos, A, Hajdu-Soltész, B, Monzon, A M, Palopoli, N, Álvarez, L, Aykac-Fas, B, Bassot, C, Benítez, G I, Bevilacqua, M, Chasapi, A, Chemes, L, Davey, N E, Davidović, R, Dunker, A K, Elofsson, A, Gobeill, J, Foutel, N S G, Sudha, G, Guharoy, M, Horvath, T, Iglesias, V, Kajava, A V, Kovacs, O P, Lamb, J, Lambrughi, M, Lazar, T, Leclercq, J Y, Leonardi, E, MacEdo-Ribeiro, S, MacOssay-Castillo, M, Maiani, E, Manso, J A, Marino-Buslje, C, Martínez-Pérez, E, Mészáros, B, Mičetić, I, Minervini, G, Murvai, N, Necci, M, Ouzounis, C A, Pajkos, M, Paladin, L, Pancsa, R, Papaleo, E, Parisi, G, Pasche, E, Barbosa Pereira, P J, Promponas, V J, Pujols, J, Quaglia, F, Ruch, P, Salvatore, M, Schad, E, Szabo, B, Szaniszló, T, Tamana, S, Tantos, A, Veljkovic, N, Ventura, S, Vranken, W, Dosztányi, Z, Tompa, P, Tosatto, S C E & Piovesan, D 2020, ' DisProt : Intrinsic protein disorder annotation in 2020 ', Nucleic Acids Research, vol. 48, no. D1, pp. D269-D276 . https://doi.org/10.1093/nar/gkz975, Hyper Article en Ligne, GNOSIS Institutional Repository, HAL-Inserm, Mémoires en Sciences de l'Information et de la Communication, Hes-so: ArODES Open Archive (University of Applied Sciences and Arts Western Switzerland, Diposit Digital de Documents de la UAB, VinaR-Repository of the Vinča Institute of Nuclear Sciences, University of Belgrade, Archivio istituzionale della ricerca-Università di Padova, European Union Open Data Portal, LAReferencia-Red Federada de Repositorios Institucionales de Publicaciones Científicas Latinoamericanas, Sygma, Datacite, UnpayWall, ORCID, Microsoft Academic Graph, PubMed Central, Copenhagen University Research Information System, Hal-Diderot
Publication Year :
2020
Publisher :
HAL CCSD, 2020.

Abstract

The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the 'dark' proteome. Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) of Argentina [PICT-2015/3367, PICT-2017/1924]; Ministry of Education, Science and Technological Development of the Republic of Serbia [ON173001]; Vetenskapsrådet [2016-03798]; Hungarian National Research, Development, and Innovation Office (NKFIH) [FK-128133]; Italian Ministry of Health Young Investigator Grant [GR-2011-02347754]; Ministerio de Economía y Competitividad (MINECO) [BIO2016-78310-R]; ICREA (ICREA-Academia 2015); Fundac¸ão para a Ciência e a Tecnologia (FCT, Portugal); European Regional Development Fund [POCI-01-0145-FEDER-031173, POCI-01-0145-FEDER-029221]; Mexican National Council of Science and Technology (CONACYT) [215503]; Elixir-GR, Action ‘Reinforcement of the Research and Innovation Infrastructure’, Operational Programme ‘Competitiveness, Entrepreneurship and Innovation’ [NSRF 2014-2020]. co-financed by Greece and the European Union (European Regional Development Fund); Hungarian Academy of Sciences [PREMIUM-2017-48]; Carlsberg Distinguished Fellowship [CF18-0314]; Danmarks Grundforskningsfond [DNRF125]; National Research, Development and Innovation Office [K-125340]; Research Foundation Flanders (FWO) [G.0328.16N]; Hungarian Academy of Sciences [LP2014-18]; OTKA [K108798 and K124670]. This project has received funding from the European Union’s Horizon 2020 research and innovation programme [778247]. Funding for open access charge: European Union’s Horizon 2020 research and innovation programme [778247]. Conflict of interest statement. None declared.

Details

Language :
English
ISSN :
03051048 and 13624962
Database :
OpenAIRE
Journal :
Nucleic Acids Research, Nucleic Acids Res., Nucleic Acids Research, Oxford University Press, 2019, ⟨10.1093/nar/gkz975⟩, Dipòsit Digital de Documents de la UAB, Universitat Autònoma de Barcelona, Hatos, A, Hajdu-Soltész, B, Monzon, A M, Palopoli, N, Álvarez, L, Aykac-Fas, B, Bassot, C, Benítez, G I, Bevilacqua, M, Chasapi, A, Chemes, L, Davey, N E, Davidović, R, Dunker, A K, Elofsson, A, Gobeill, J, Foutel, N S G, Sudha, G, Guharoy, M, Horvath, T, Iglesias, V, Kajava, A V, Kovacs, O P, Lamb, J, Lambrughi, M, Lazar, T, Leclercq, J Y, Leonardi, E, MacEdo-Ribeiro, S, MacOssay-Castillo, M, Maiani, E, Manso, J A, Marino-Buslje, C, Martínez-Pérez, E, Mészáros, B, Mičetić, I, Minervini, G, Murvai, N, Necci, M, Ouzounis, C A, Pajkos, M, Paladin, L, Pancsa, R, Papaleo, E, Parisi, G, Pasche, E, Barbosa Pereira, P J, Promponas, V J, Pujols, J, Quaglia, F, Ruch, P, Salvatore, M, Schad, E, Szabo, B, Szaniszló, T, Tamana, S, Tantos, A, Veljkovic, N, Ventura, S, Vranken, W, Dosztányi, Z, Tompa, P, Tosatto, S C E & Piovesan, D 2020, ' DisProt : Intrinsic protein disorder annotation in 2020 ', Nucleic Acids Research, vol. 48, no. D1, pp. D269-D276 . https://doi.org/10.1093/nar/gkz975, Hyper Article en Ligne, GNOSIS Institutional Repository, HAL-Inserm, Mémoires en Sciences de l'Information et de la Communication, Hes-so: ArODES Open Archive (University of Applied Sciences and Arts Western Switzerland, Diposit Digital de Documents de la UAB, VinaR-Repository of the Vinča Institute of Nuclear Sciences, University of Belgrade, Archivio istituzionale della ricerca-Università di Padova, European Union Open Data Portal, LAReferencia-Red Federada de Repositorios Institucionales de Publicaciones Científicas Latinoamericanas, Sygma, Datacite, UnpayWall, ORCID, Microsoft Academic Graph, PubMed Central, Copenhagen University Research Information System, Hal-Diderot
Accession number :
edsair.doi.dedup.....bd4170a83588920eb94425162ce0c585
Full Text :
https://doi.org/10.1093/nar/gkz975⟩