Literature DB >> 31713636

DisProt: intrinsic protein disorder annotation in 2020.

András Hatos1, Borbála Hajdu-Soltész2, Alexander M Monzon1, Nicolas Palopoli3, Lucía Álvarez4, Burcu Aykac-Fas5, Claudio Bassot6, Guillermo I Benítez3, Martina Bevilacqua1, Anastasia Chasapi7, Lucia Chemes4,8, Norman E Davey9, Radoslav Davidović10, A Keith Dunker11, Arne Elofsson6, Julien Gobeill12, Nicolás S González Foutel4, Govindarajan Sudha6, Mainak Guharoy13,14, Tamas Horvath15, Valentin Iglesias16, Andrey V Kajava17,18, Orsolya P Kovacs15, John Lamb6, Matteo Lambrughi5, Tamas Lazar13,14, Jeremy Y Leclercq17, Emanuela Leonardi19,20, Sandra Macedo-Ribeiro21, Mauricio Macossay-Castillo13,14, Emiliano Maiani5, José A Manso21, Cristina Marino-Buslje22, Elizabeth Martínez-Pérez22, Bálint Mészáros2, Ivan Mičetić1, Giovanni Minervini1, Nikoletta Murvai15, Marco Necci1, Christos A Ouzounis7, Mátyás Pajkos2, Lisanna Paladin1, Rita Pancsa15, Elena Papaleo5,23, Gustavo Parisi3, Emilie Pasche12, Pedro J Barbosa Pereira21, Vasilis J Promponas24, Jordi Pujols16, Federica Quaglia1, Patrick Ruch12, Marco Salvatore6, Eva Schad15, Beata Szabo15, Tamás Szaniszló2, Stella Tamana24, Agnes Tantos15, Nevena Veljkovic10, Salvador Ventura16, Wim Vranken13,14,25, Zsuzsanna Dosztányi2, Peter Tompa13,14,15, Silvio C E Tosatto1,26, Damiano Piovesan1.   

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.
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Year:  2020        PMID: 31713636      PMCID: PMC7145575          DOI: 10.1093/nar/gkz975

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  38 in total

1.  Unexpected features of the dark proteome.

Authors:  Nelson Perdigão; Julian Heinrich; Christian Stolte; Kenneth S Sabir; Michael J Buckley; Bruce Tabor; Beth Signal; Brian S Gloss; Christopher J Hammang; Burkhard Rost; Andrea Schafferhans; Seán I O'Donoghue
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-17       Impact factor: 11.205

2.  Large-scale analysis of intrinsic disorder flavors and associated functions in the protein sequence universe.

Authors:  Marco Necci; Damiano Piovesan; Silvio C E Tosatto
Journal:  Protein Sci       Date:  2016-10-25       Impact factor: 6.725

3.  Structural disorder of monomeric α-synuclein persists in mammalian cells.

Authors:  Francois-Xavier Theillet; Andres Binolfi; Beata Bekei; Andrea Martorana; Honor May Rose; Marchel Stuiver; Silvia Verzini; Dorothea Lorenz; Marleen van Rossum; Daniella Goldfarb; Philipp Selenko
Journal:  Nature       Date:  2016-01-25       Impact factor: 49.962

4.  Structure and mechanism of human UDP-glucose 6-dehydrogenase.

Authors:  Sigrid Egger; Apirat Chaikuad; Kathryn L Kavanagh; Udo Oppermann; Bernd Nidetzky
Journal:  J Biol Chem       Date:  2011-04-18       Impact factor: 5.157

5.  Corrigendum: DisProt 7.0: a major update of the database of disordered proteins.

Authors:  Damiano Piovesan; Francesco Tabaro; Ivan Mičetić; Marco Necci; Federica Quaglia; Christopher J Oldfield; Maria Cristina Aspromonte; Norman E Davey; Radoslav Davidović; Zsuzsanna Dosztányi; Arne Elofsson; Alessandra Gasparini; András Hatos; Andrey V Kajava; Lajos Kalmar; Emanuela Leonardi; Tamas Lazar; Sandra Macedo-Ribeiro; Mauricio Macossay-Castillo; Attila Meszaros; Giovanni Minervini; Nikoletta Murvai; Jordi Pujols; Daniel B Roche; Edoardo Salladini; Eva Schad; Antoine Schramm; Beata Szabo; Agnes Tantos; Fiorella Tonello; Konstantinos D Tsirigos; Nevena Veljković; Salvador Ventura; Wim Vranken; Per Warholm; Vladimir N Uversky; A Keith Dunker; Sonia Longhi; Peter Tompa; Silvio C E Tosatto
Journal:  Nucleic Acids Res       Date:  2016-12-13       Impact factor: 16.971

6.  The entropic force generated by intrinsically disordered segments tunes protein function.

Authors:  Nicholas D Keul; Krishnadev Oruganty; Elizabeth T Schaper Bergman; Nathaniel R Beattie; Weston E McDonald; Renuka Kadirvelraj; Michael L Gross; Robert S Phillips; Stephen C Harvey; Zachary A Wood
Journal:  Nature       Date:  2018-11-12       Impact factor: 49.962

Review 7.  The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease.

Authors:  M Madan Babu
Journal:  Biochem Soc Trans       Date:  2016-10-15       Impact factor: 5.407

8.  Gene3D: Extensive prediction of globular domains in proteins.

Authors:  Tony E Lewis; Ian Sillitoe; Natalie Dawson; Su Datt Lam; Tristan Clarke; David Lee; Christine Orengo; Jonathan Lees
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

9.  DIBS: a repository of disordered binding sites mediating interactions with ordered proteins.

Authors:  Eva Schad; Erzsébet Fichó; Rita Pancsa; István Simon; Zsuzsanna Dosztányi; Bálint Mészáros
Journal:  Bioinformatics       Date:  2018-02-01       Impact factor: 6.937

10.  The Pfam protein families database in 2019.

Authors:  Sara El-Gebali; Jaina Mistry; Alex Bateman; Sean R Eddy; Aurélien Luciani; Simon C Potter; Matloob Qureshi; Lorna J Richardson; Gustavo A Salazar; Alfredo Smart; Erik L L Sonnhammer; Layla Hirsh; Lisanna Paladin; Damiano Piovesan; Silvio C E Tosatto; Robert D Finn
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

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  67 in total

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Authors:  Benjamin Lang; M Madan Babu
Journal:  Nat Methods       Date:  2021-04-19       Impact factor: 28.547

2.  IDPology of the living cell: intrinsic disorder in the subcellular compartments of the human cell.

Authors:  Bi Zhao; Akila Katuwawala; Vladimir N Uversky; Lukasz Kurgan
Journal:  Cell Mol Life Sci       Date:  2020-09-30       Impact factor: 9.261

3.  Predicting Protein Conformational Disorder and Disordered Binding Sites.

Authors:  Ketty C Tamburrini; Giulia Pesce; Juliet Nilsson; Frank Gondelaud; Andrey V Kajava; Jean-Guy Berrin; Sonia Longhi
Journal:  Methods Mol Biol       Date:  2022

Review 4.  Current status of PTMs structural databases: applications, limitations and prospects.

Authors:  Alexandre G de Brevern; Joseph Rebehmed
Journal:  Amino Acids       Date:  2022-01-12       Impact factor: 3.520

5.  The dynamic basis of structural order in proteins.

Authors:  Chilaluck Konkankit; S Rackovsky
Journal:  Proteins       Date:  2022-01-11

6.  Self-assembly of globular proteins with intrinsically disordered protein polyelectrolytes and block copolymers.

Authors:  Justin M Horn; Yuncan Zhu; So Yeon Ahn; Allie C Obermeyer
Journal:  Soft Matter       Date:  2022-08-10       Impact factor: 4.046

7.  Homopeptide and homocodon levels across fungi are coupled to GC/AT-bias and intrinsic disorder, with unique behaviours for some amino acids.

Authors:  Yue Wang; Paul M Harrison
Journal:  Sci Rep       Date:  2021-05-11       Impact factor: 4.379

8.  Evolutionary conservation of intrinsically unstructured regions in slit-diaphragm proteins.

Authors:  Sandeep K N Mulukala; Vaishnavi Kambhampati; Abrar H Qadri; Anil K Pasupulati
Journal:  PLoS One       Date:  2021-07-21       Impact factor: 3.240

9.  IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation.

Authors:  Gábor Erdős; Mátyás Pajkos; Zsuzsanna Dosztányi
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

10.  flDPnn: Accurate intrinsic disorder prediction with putative propensities of disorder functions.

Authors:  Gang Hu; Akila Katuwawala; Kui Wang; Zhonghua Wu; Sina Ghadermarzi; Jianzhao Gao; Lukasz Kurgan
Journal:  Nat Commun       Date:  2021-07-21       Impact factor: 14.919

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