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Driving the functional characterization of intrinsically disordered proteins

Deliverables

Software to discriminate different types of disorder based on amino acid propensities and other features

Software to discriminate different types of disorder based on amino acid propensities and other features.

Software package for the automatic extraction of PED entry data from protein ensembles

Software package for the automatic extraction of PED entry data from protein ensembles.

New version of the Mobi software

New version of the Mobi software.

Software for the identification of homologous IDR clusters from sequence databases

Software for the identification of homologous IDR clusters from sequence databases.

A software tool for the automatic extraction of IDR relevant information from literature

A software tool for the automatic extraction of IDR relevant information from literature.

Software for automatic detection of IDRs and linear motifs from protein structures

Software pipeline for the automatic extraction of X-ray derived IDR information (missing electron densities), linear motifs and consensus generation.

Symposia Period 1

Twice in Europe: Administrative visit. ESR symposium. Scientific symposium. Hackathon. Train-the-trainers. Transferable skills symposium. Career development. SB and AB meeting. Twice in Argentina: ESR Symposium. Training bootcamp. SB meeting. Public outreach activities.

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Publications

Exploring Curated Conformational Ensembles of Intrinsically Disordered Proteins in the Protein Ensemble Database

Author(s): Federica Quaglia; Federica Quaglia; Tamas Lazar; András Hatos; Peter Tompa; Damiano Piovesan; Silvio C. E. Tosatto
Published in: Current Protocols, 26911299, 2021, ISSN 2691-1299
Publisher: John Wiley and Sons Inc
DOI: 10.1002/cpz1.192

MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins

Author(s): Marco Necci; Damiano Piovesan; Damiano Clementel; Zsuzsanna Dosztányi; Silvio C. E. Tosatto
Published in: Bioinformatics, 13674803, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1045

Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank.

Author(s): Alexander Miguel Monzon; Marco Necci; Federica Quaglia; Ian Walsh; Damiano Piovesan; Giuseppe Zanotti; Silvio C. E. Tosatto
Published in: International Journal of Molecular Sciences, 14220067, 2020, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms21124496

SARS‐CoV‐2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion

Author(s): Federica Quaglia; Edoardo Salladini; Marco Carraro; Giovanni Minervini; Silvio C.E. Tosatto; Philippe Le Mercier
Published in: FEBS Journal, 1742464X, 2022, ISSN 1742-464X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/febs.16379

The Eukaryotic Linear Motif resource: 2022 release

Author(s): Manjeet Kumar; Sushama Michael; Jesús Alvarado-Valverde; Bálint Mészáros; Hugo Sámano-Sánchez; Hugo Sámano-Sánchez; András Zeke; László Dobson; Tamas Lazar; Tamas Lazar; Mihkel Örd; Anurag Nagpal; Nazanin Farahi; Nazanin Farahi; Melanie Käser; Ramya Kraleti; Norman E. Davey; Rita Pancsa; Lucía B. Chemes; Toby J. Gibson
Published in: Nucleic Acids Research, 03051048, 2022, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab975

PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins.

Author(s): Patryk Jarnot; Joanna Ziemska-Legiecka; László Dobson; Matthew Merski; Pablo Mier; Miguel A. Andrade-Navarro; John M. Hancock; Zsuzsanna Dosztányi; Lisanna Paladin; Marco Necci; Damiano Piovesan; Silvio C. E. Tosatto; Vasilis J. Promponas; Marcin Grynberg; Aleksandra Gruca
Published in: Nucleic Acids Research, 03051048, 2020, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa339

ELM-the eukaryotic linear motif resource in 2020.

Author(s): Kumar, Manjeet; Gouw, Marc; Michael, Sushama; Sámano-Sánchez, Hugo; Pancsa, Rita; Glavina, Juliana; Diakogianni, Athina; Valverde, Jesús Alvarado; Bukirova, Dayana; Čalyševa, Jelena; Palopoli, Nicolas; Davey, Norman E; Chemes, Lucía B; Gibson, Toby J
Published in: Nucleic Acids Research, 03051048, 2020, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz1030

An intrinsically disordered proteins community for ELIXIR.

Author(s): Davey, Norman E.; Babu, M. Madan; Blackledge, Martin; Bridge, Alan; Capella-Gutierrez, Salvador; Dosztanyi, Zsuzsanna; Drysdale, Rachel; Edwards, Richard J.; Elofsson, Arne; Felli, Isabella C.; Gibson, Toby J.; Gutmanas, Aleksandras; Hancock, John M.; Harrow, Jen; Higgins, Desmond; Jeffries, Cy M.; Le Mercier, Philippe; Mészáros, Balint; Necci, Marco; Notredame, Cedric; Orchard, Sandra; Ouzounis
Published in: F1000Research, 20461402, 2019, ISSN 2046-1402
Publisher: F1000 Research Ltd.
DOI: 10.12688/f1000research.20136.1

APICURON: a database to credit and acknowledge the work of biocurators

Author(s): András Hatos; Federica Quaglia; Damiano Piovesan; Silvio C. E. Tosatto
Published in: Database: The Journal of Biological Databases and Curation, 17580463, 2021, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/baab019

Databases for intrinsically disordered proteins

Author(s): Damiano Piovesan; Alexander Miguel Monzon; Federica Quaglia; Silvio C. E. Tosatto
Published in: Acta Crystallographica Section D: Structural Biology, 20597983, 2022, ISSN 2059-7983
Publisher: Wiley-Blackwell
DOI: 10.1107/s2059798321012109

Conference report: Biocuration 2021 Virtual Conference

Author(s): Federica Quaglia; Rama Balakrishnan; Susan M Bello; Nicole Vasilevsky
Published in: Database, 17580463, 2021, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/baac027

The Feature-Viewer: a visualization tool for positional annotations on a sequence

Author(s): Lisanna Paladin; Mathieu Schaeffer; Pascale Gaudet; Monique Zahn-Zabal; Pierre-André Michel; Damiano Piovesan; Silvio C. E. Tosatto; Amos Marc Bairoch
Published in: Bioinformatics, 13674803, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa055

Critical assessment of protein intrinsic disorder prediction

Author(s): Necci, Marco; Piovesan, Damiano; Hoque Md, Tamjidul; Walsh, Ian; Iqbal, Sumaiya; Vendruscolo, Michele; Sormanni, Pietro; Wang, Chen; Raimondi, Daniele; Sharma, Ronesh; Zhou, Yaoqi; Litfin, Thomas; Galzitskaya Oxana, Valerianovna; Lobanov Michail, Yu; Vranken, Wim; Wallner, Björn; Mirabello, Claudio; Malhis, Nawar; Dosztányi, Zsuzsanna; Erdős, Gábor; Mészáros, Bálint; Gao, Jianzhao; Wang, Ku
Published in: Nature Methods, 15487091, 2021, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-021-01117-3

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

Author(s): Tamas Lazar; Tamas Lazar; Elizabeth Martínez-Pérez; Federica Quaglia; András Hatos; Lucía B. Chemes; Javier Iserte; Nicolás A. Méndez; Nicolás A. Garrone; Tadeo E. Saldaño; Julia Marchetti; Ana Julia Velez Rueda; Pau Bernadó; Martin Blackledge; Tiago N. Cordeiro; Tiago N. Cordeiro; Eric Fagerberg; Julie D. Forman-Kay; María Silvina Fornasari; Toby J. Gibson; Gregory-Neal W. Gomes; Claudi
Published in: Nucleic Acids Research, 03051048, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa1021

Prediction of polyproline II secondary structure propensity in proteins.

Author(s): Kevin T. O’Brien; Catherine Mooney; Cyril Lopez; Gianluca Pollastri; Denis C. Shields
Published in: Royal Society Open Science, 20545703, 2020, ISSN 2054-5703
Publisher: Royal Society Publishing
DOI: 10.1098/rsos.191239

"""Protein"" no longer means what it used to."

Author(s): Gustavo Parisi; Nicolas Palopoli; Silvio C. E. Tosatto; María Silvina Fornasari; Peter Tompa
Published in: Current Research in Structural Biology, 2665928X, 2021, ISSN 2665-928X
Publisher: Elsevier B.V.
DOI: 10.1016/j.crstbi.2021.06.002

Molecular Determinants of Selectivity in Disordered Complexes May Shed Light on Specificity in Protein Condensates

Author(s): Alexander Miguel Monzon; Damiano Piovesan; Monika Fuxreiter
Published in: Biomolecules, 2218273X, 2022, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12010092

DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.

Author(s): Federica Quaglia; Federica Quaglia; Bálint Mészáros; Edoardo Salladini; András Hatos; Rita Pancsa; Lucía B. Chemes; Mátyás Pajkos; Tamas Lazar; Tamas Lazar; Samuel Peña-Díaz; Jaime Santos; Veronika Ács; Nazanin Farahi; Nazanin Farahi; Erzsébet Fichó; Maria Cristina Aspromonte; Claudio Bassot; Anastasia Chasapi; Norman E. Davey; Radoslav Davidovic; László Dobson; Arne Elofsson; Gábor
Published in: Nucleic Acids Research, 03051048, 2022, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1082

Assessing predictors for new post translational modification sites: a case study on hydroxylation

Author(s): Damiano Piovesan; András Hatos; Giovanni Minervini; Federica Quaglia; Alexander Miguel Monzon; Silvio C. E. Tosatto
Published in: PLoS Computational Biology, 1553734X, 2020, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1007967

Where differences resemble: sequence-feature analysis in curated databases of intrinsically disordered proteins

Author(s): Marco Necci, Damiano Piovesan, Silvio C E Tosatto
Published in: Database, 2018, 2018, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/bay127

Disentangling the complexity of low complexity proteins

Author(s): Pablo Mier, Lisanna Paladin, Stella Tamana, Sophia Petrosian, Borbála Hajdu-Soltész, Annika Urbanek, Aleksandra Gruca, Dariusz Plewczynski, Marcin Grynberg, Pau Bernadó, Zoltán Gáspári, Christos A Ouzounis, Vasilis J Promponas, Andrey V Kajava, John M Hancock, Silvio C E Tosatto, Zsuzsanna Dosztanyi, Miguel A Andrade-Navarro
Published in: Briefings in Bioinformatics, 2019, 2019, ISSN 1467-5463
Publisher: Oxford University Press
DOI: 10.1093/bib/bbz007

Ensembles from Ordered and Disordered Proteins Reveal Similar Structural Constraints during Evolution

Author(s): Julia Marchetti, Alexander Miguel Monzon, Silvio C.E. Tosatto, Gustavo Parisi, María Silvina Fornasari
Published in: Journal of Molecular Biology, 431/6, 2019, Page(s) 1298-1307, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2019.01.031

INGA 2.0: improving protein function prediction for the dark proteome

Author(s): Damiano Piovesan, Silvio C E Tosatto
Published in: Nucleic Acids Research, 47/W1, 2019, Page(s) W373-W378, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz375

DisProt: intrinsic protein disorder annotation in 2020

Author(s): András Hatos, Borbála Hajdu-Soltész, Alexander M Monzon, Nicolas Palopoli, Lucía Álvarez, Burcu Aykac-Fas, Claudio Bassot, Guillermo I Benítez, Martina Bevilacqua, Anastasia Chasapi, Lucia Chemes, Norman E Davey, Radoslav Davidović, A Keith Dunker, Arne Elofsson, Julien Gobeill, Nicolás S González Foutel, Govindarajan Sudha, Mainak Guharoy, Tamas Horvath, Valentin Iglesias, Andrey V Kaj
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz975

PhaSePro: the database of proteins driving liquid–liquid phase separation

Author(s): Bálint Mészáros, Gábor Erdős, Beáta Szabó, Éva Schád, Ágnes Tantos, Rawan Abukhairan, Tamás Horváth, Nikoletta Murvai, Orsolya P Kovács, Márton Kovács, Silvio C E Tosatto, Péter Tompa, Zsuzsanna Dosztányi, Rita Pancsa
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz848

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Author(s): Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Ge
Published in: Genome Biology, 20/1, 2019, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1186/s13059-019-1835-8

ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications.

Author(s): Martina Bevilacqua; Lisanna Paladin; Silvio C. E. Tosatto; Damiano Piovesan
Published in: Bioinformatics, 13674803, 2021, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab764

Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications.

Author(s): Bálint Mészáros; Hugo Sámano-Sánchez; Jesús Alvarado-Valverde; Jelena Čalyševa; Elizabeth Martínez-Pérez; Renato J. Alves; Denis C. Shields; Manjeet Kumar; Friedrich Rippmann; Lucía B. Chemes; Toby J. Gibson
Published in: Science Signaling, 19450877, 2021, ISSN 1945-0877
Publisher: American Association for the Advancement of Science
DOI: 10.1126/scisignal.abd0334

Chasing coevolutionary signals in intrinsically disordered proteins complexes

Author(s): Javier Iserte; Tamas Lazar; Silvio C. E. Tosatto; Peter Tompa; Peter Tompa; Cristina Marino-Buslje
Published in: Scientific Reports, 20452322, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-74791-6

Supplementary Data and Figures from Prediction of polyproline II secondary structure propensity in proteins

Author(s): O’Brien, Kevin T.; Mooney, Catherine; Lopez, Cyril; Pollastri, Gianluca; Shields, Denis C.
Published in: Figshare, 2020
Publisher: Figshare
DOI: 10.6084/m9.figshare.11547267.v1

MOESM1 of The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Author(s): Naihui Zhou; Yuxiang Jiang; Bergquist, Timothy; Lee, Alexandra; Balint Kacsoh; Crocker, Alex; Lewis, Kimberley; Georghiou, George; Nguyen, Huy; Md Nafiz Hamid; Davis, Larry; Tunca Dogan; Atalay, Volkan; Rifaioglu, Ahmet; Dalkıran, Alperen; Rengul Cetin Atalay; Chengxin Zhang; Hurto, Rebecca; Freddolino, Peter; Zhang, Yang; Prajwal Bhat; Supek, Fran; Fernández, José; Gemovic, Branislava; Perovic
Published in: 2020
Publisher: Figshare
DOI: 10.6084/m9.figshare.10458494.v1

MOESM2 of The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Author(s): Naihui Zhou; Yuxiang Jiang; Bergquist, Timothy; Lee, Alexandra; Balint Kacsoh; Crocker, Alex; Lewis, Kimberley; Georghiou, George; Nguyen, Huy; Md Nafiz Hamid; Davis, Larry; Tunca Dogan; Atalay, Volkan; Rifaioglu, Ahmet; Dalkıran, Alperen; Rengul Cetin Atalay; Chengxin Zhang; Hurto, Rebecca; Freddolino, Peter; Zhang, Yang; Prajwal Bhat; Supek, Fran; Fernández, José; Gemovic, Branislava; Perovic
Published in: 2020
Publisher: Figshare
DOI: 10.6084/m9.figshare.10458518.v1