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Driving the functional characterization of intrinsically disordered proteins

Deliverables

Integration of ID data generated in WP1 and WP2 into MobiDB

Integration of IDR data generated in WP1 and WP2 into MobiDB.

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.

Cross-link of generated IDR data into core resources (InterPro, UniProt)

Cross-link of generated IDR data into core resources (InterPro, UniProt).

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.

Symposia period 2

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

Publications

Intrinsic protein disorder uncouples affinity from binding specificity

Author(s): Lazar T, Tantos A, Tompa P, Schad E
Published in: Protein Science, 2022, ISSN 0961-8368
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1002/pro.4455

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, Issue 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, Issue 13674803, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1045

Pipeline for transferring annotations between proteins beyond globular domains

Author(s): Martínez-Pérez E, Pajkos M, Tosatto SCE, Gibson TJ, Dosztanyi Z, Marino- Buslje C
Published in: Protein Science, 2023, ISSN 0961-8368
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1002/pro.4655

The sequence context in poly-alanine regions: structure, function and conservation

Author(s): Mier, Pablo; Elena-Real, Carlos A; Cortés, Juan; Bernadó, Pau; Andrade-Navarro, Miguel A
Published in: Bioinformatics, 2022, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac610

Analyzing Protein Disorder with IUPred2A

Author(s): Gábor Erdős, Zsuzsanna Dosztányi
Published in: Current Protocols in Bioinformatics, 2020, ISSN 1934-3396
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/cpbi.99

The evolution and polymorphism of mono-amino acid repeats in androgen receptor and their regulatory role in health and disease

Author(s): Meszaros A, Ahmed J, Russo G, Tompa P, Lazar T
Published in: Frontiers in Medicine, 2022, ISSN 2296-858X
Publisher: Frontiers Media
DOI: 10.3389/fmed.2022.1019803

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins

Author(s): Del Conte A, Bouhraoua A, Mehdiabadi M, Clementel D, Monzon AM; CAID predictors; Tosatto SCE, Piovesan D
Published in: Nucleic Acids Research, 2023, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad430

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, Issue 14220067, 2020, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms21124496

DOME: recommendations for supervised machine learning validation in biology

Author(s): Walsh I, Fishman D, Garcia-Gasulla D, Titma T, Pollastri G; ELIXIR Machine Learning Focus Group; Harrow J, Psomopoulos FE, Tosatto SCE
Published in: Nature Methods, 2021, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-021-01205-4

Impact of protein conformational diversity on AlphaFold predictions

Author(s): Tadeo Saldaño, Nahuel Escobedo, Julia Marchetti, Diego Javier Zea, Juan Mac Donagh, Ana Julia Velez Rueda, Eduardo Gonik, Agustina García Melani, Julieta Novomisky Nechcoff, Martín N Salas, Tomás Peters, Nicolás Demitroff, Sebastian Fernandez Alberti, Nicolas Palopoli, Maria Silvina Fornasari, Gustavo Parisi
Published in: Bioinformatics, 2022, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac202

FLIPPER: Predicting and Characterizing Linear Interacting Peptides in the Protein Data Bank

Author(s): Alexander Miguel Monzon, Paolo Bonato, Marco Necci, Silvio C.E. Tosatto, Damiano Piovesan
Published in: Journal of Molecular Biology, 2021, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2021.166900

Intrinsically Disordered Protein Ensembles Shape Evolutionary Rates Revealing Conformational Patterns

Author(s): Nicolás Palopoli, Julia Marchetti, Alexander Miguel Monzon, Diego J. Zea, Silvio C. E. Tosatto, María Silvina Fornasari, Gustavo Parisi.
Published in: Journal of Molecular Biology, 2021, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2020.166751

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, Issue 1742464X, 2022, ISSN 1742-464X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/febs.16379

Degron masking outlines degronons, co-degrading functional modules in the proteome

Author(s): Guharoy M, Lazar T, Macossay-Castillo M, Tompa P
Published in: Communications Biology, 2022, ISSN 2399-3642
Publisher: Nature Publishing Group
DOI: 10.1038/s42003-022-03391-z

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, Issue 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, Issue 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, Issue 03051048, 2020, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz1030

MobiDB: intrinsically disordered proteins in 2021.

Author(s): Damiano Piovesan; Marco Necci; Nahuel Escobedo; Alexander Miguel Monzon; András Hatos; Ivan Mičetić; Federica Quaglia; Lisanna Paladin; Pathmanaban Ramasamy; Zsuzsanna Dosztányi; Wim F. Vranken; Norman E. Davey; Gustavo Parisi; Monika Fuxreiter; Silvio C. E. Tosatto
Published in: Nucleic Acids Research, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa1058

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, Issue 20461402, 2019, ISSN 2046-1402
Publisher: F1000 Research Ltd.
DOI: 10.12688/f1000research.20136.1

Exploring Conformational Space with Thermal Fluctuations Obtained by Normal-Mode Analysis.

Author(s): Tadeo E. Saldaño; Victor M. Freixas; Silvio C. E. Tosatto; Gustavo Parisi; Sebastian Fernandez-Alberti
Published in: JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2020, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.9b01136

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, Issue 17580463, 2021, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/baab019

CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure

Author(s): Escobedo N, Tunque Cahui RR, Caruso G, García Ríos E, Hirsh L, Monzon AM, Parisi G, Palopoli N
Published in: Bioinformatics, 2022, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac627

Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions

Author(s): Mészáros B, Hatos A, Palopoli N, Quaglia F, Salladini E, Van Roey K, Arthanari H, Dosztányi Z, Felli IC, Fischer PD, Hoch JC, Jeffries CM, Longhi S, Maiani E, Orchard S, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Pritisanac I, Tenorio L, Viennet T, Tompa P, Vranken W, Tosatto SCE, Davey NE
Published in: Nature Methods, 2023, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-023-01915-x

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, Issue 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, Issue 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, Issue 13674803, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa055

A fish herpesvirus highlights functional diversities among Zα domains related to phase separation induction and A-to-Z conversion

Author(s): Mamadou Amadou Diallo; Sébastien Pirotte; Yunlong Hu; Léa Morvan; Krzysztof Rakus; Nicolás M Suárez; Lee PoTsang; Hisao Saneyoshi; Yan Xu; Andrew J Davison; Peter Tompa; Joel L Sussman; Alain Vanderplasschen
Published in: Nucleic Acids Research, 2023, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac761

Combining Protein Conformational Diversity and Phylogenetic Information Using CoDNaS and CoDNaS-Q

Author(s): Escobedo N, Monzon AM, Fornasari MS, Palopoli N, Parisi G
Published in: Current protocols, 2023, ISSN 2691-1299
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/cpz1.764

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, Issue 15487091, 2021, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-021-01117-3

DisCanVis: Visualizing integrated structural and functional annotations to better understand the effect of cancer mutations located within disordered proteins

Author(s): Deutsch N, Pajkos M, Erdős G, Dosztányi Z
Published in: Protein Science, 2023, ISSN 0961-8368
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1002/pro.4522

Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt

Author(s): Federica Quaglia; András Hatos; Edoardo Salladini; Damiano Piovesan; Silvio C. E. Tosatto
Published in: Current Protocols in Bioinformatics, 2022, ISSN 1934-3396
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/cpz1.484

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, Issue 03051048, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa1021

Structural basis for tunable affinity and specificity of LxCxE-dependent protein interactions with the retinoblastoma protein family

Author(s): Putta S, Alvarez L, Lüdtke S, Sehr P, Müller GA, Fernandez SM, Tripathi S, Lewis J, Gibson TJ, Chemes LB, Rubin SM.
Published in: Structure, 2022, ISSN 0969-2126
Publisher: Cell Press
DOI: 10.1016/j.str.2022.05.019

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, Issue 20545703, 2020, ISSN 2054-5703
Publisher: Royal Society Publishing
DOI: 10.1098/rsos.191239

Intrinsic protein disorder and conditional folding in AlphaFoldDB.

Author(s): Damiano Piovesan; Alexander Miguel Monzon; Silvio C. E. Tosatto
Published in: Protein Science, 2022, ISSN 0961-8368
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1002/pro.4466

"""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, Issue 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, Issue 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, Issue 03051048, 2022, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1082

ECO: the Evidence and Conclusion Ontology, an update for 2022

Author(s): Nadendla S, Jackson R, Munro J, Quaglia F, Mészáros B, Olley D, Hobbs ET, Goralski SM, Chibucos M, Mungall CJ, Tosatto SCE, Erill I, Giglio MG
Published in: Nadendla S, Jackson R, Munro J, Quaglia F, Mészáros B, Olley D, Hobbs ET, Goralski SM, Chibucos M, Mungall CJ, Tosatto SCE, Erill I, Giglio MG, 2022, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1025

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, Issue 1553734X, 2020, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1007967

RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics

Author(s): Alessio Del Conte; Alexander Miguel Monzon; Damiano Clementel; Giorgia F Camagni; Giovanni Minervini; Silvio C E Tosatto; Damiano Piovesan
Published in: Bioinformatics, 2023, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btad260

The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification

Author(s): Nicolás Palopoli, Javier A. Iserte, Lucia B. Chemes, Cristina Marino-Buslje, Gustavo Parisi, Toby J. Gibson, Norman E. Davey
Published in: Database, 2020, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/baaa040

MobiDB: 10 years of intrinsically disordered proteins

Author(s): Damiano Piovesan; Alessio Del Conte; Damiano Clementel; Alexander Miguel Monzon; Martina Bevilacqua; Maria Cristina Aspromonte; Javier A Iserte; Fernando E Orti; Cristina Marino-Buslje; Silvio C E Tosatto
Published in: Nucleic Acids Research, 2022, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac1065

Critical assessment of protein intrinsic disorder prediction (CAID) - Results of round 2

Author(s): Conte AD, Mehdiabadi M, Bouhraoua A, Miguel Monzon A, Tosatto SCE, Piovesan D
Published in: Proteins: Structure, Function and Bioinformatics, 2023, ISSN 0887-3585
Publisher: Wiley-Liss Inc
DOI: 10.1002/prot.26582

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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 20/1, 2019, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1186/s13059-019-1835-8

A Novel Tandem-Tag Purification Strategy for Challenging Disordered Proteins

Author(s): Mészáros A, Muwonge K, Janvier S, Ahmed J, Tompa P
Published in: Biomolecules, 2022, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12111566

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, Issue 13674803, 2021, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab764

F/YGG-motif is an intrinsically disordered nucleic-acid binding motif

Author(s): Van Lindt J, Lazar T, Pakravan D, Demulder M, Meszaros A, Van Den Bosch L, Maes D, Tompa P
Published in: RNA Biology, 2022, ISSN 1547-6286
Publisher: Landes Bioscience
DOI: 10.1080/15476286.2022.2066336

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, Issue 19450877, 2021, ISSN 1945-0877
Publisher: American Association for the Advancement of Science
DOI: 10.1126/scisignal.abd0334

FuzDB: A new phase in understanding fuzzy interactions

Author(s): Hatos A, Monzon AM, Tosatto SCE, Piovesan D, Fuxreiter M
Published in: Nucleic Acids Research, 2022, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1060

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, Issue 20452322, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-74791-6

RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles

Author(s): Clementel D, Del Conte A, Monzon AM, Camagni GF, Minervini G, Piovesan D, Tosatto SCE.
Published in: Nucleic Acids Research, 2022, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac365

Proteomics Standards Initiative at twenty years : current activities and future work

Author(s): Eric W. Deutsch; Juan Antonio Vizcaíno; Andrew R. Jones; Pierre-Alain Binz; Henry Lam; Joshua Klein; Wout Bittremieux; Yasset Perez-Riverol; David L. Tabb; Mathias Walzer; Sylvie Ricard-Blum; Henning Hermjakob; Steffen Neumann; Tytus D. Mak; Shin Kawano; Luis Mendoza; Tim Van Den Bossche; Ralf Gabriels; Nuno Bandeira; Jeremy Carver; Benjamin Pullman; Zhi Sun; Nils Hoffmann; Jim Shofstahl; Yunping
Published in: Journal of proteome research, 2023, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00637

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

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