H2020 MSCA-RISE project

Project acknowledgement

IDPfun is supported by the European Union through the Marie Curie Actions, in the context of the research and innovation program Horizon 2020. EU support shall be acknowledged in all outputs of the project (such as publications, dissemination materials, thesis, journal articles, reach-out activities, etc.) with the following statement:

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 778247.

When possible, the statement shall be associated to the EU emblem, as exampled above. When displayed together with another logo, the EU emblem must have appropriate prominence.

Scientific publications

  • 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, MobiDB: 10 years of intrinsically disordered proteins, Nucleic Acids Research, Volume 51, Issue D1, Pages D438–D444 (2023).
  • Alessio Del Conte, Alexander Miguel Monzon, Damiano Clementel, Giorgia F Camagni, Giovanni Minervini, Silvio C E Tosatto, Damiano Piovesan, RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics, Bioinformatics, Volume 39, Issue 5 (2023).
  • Deutsch EW, Vizcaíno JA, Jones AR, Binz PA, Lam H, Klein J, Bittremieux W, Perez-Riverol Y, Tabb DL, Walzer M, Ricard-Blum S, Hermjakob H, Neumann S, Mak TD, Kawano S, Mendoza L, Van Den Bossche T, Gabriels R, Bandeira N, Carver J, Pullman B, Sun Z, Hoffmann N, Shofstahl J, Zhu Y, Licata L, Quaglia F, Tosatto SCE, Orchard SE., Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work, Journal of Proteome Research, 22, 2, 287–301 (2023).
  • 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, A fish herpesvirus highlights functional diversities among Zα domains related to phase separation induction and A-to-Z conversion, Nucleic Acids Research, Volume 51, Issue 2, Pages 806–830 (2023).
  • Alexander Miguel Monzon Damiano Piovesan Monika Fuxreiter, Molecular Determinants of Selectivity in Disordered Complexes May Shed Light on Specificity in Protein Condensates, Biomolecules, 12(1), 92 (2022).
  • Federica Quaglia,Edoardo Salladini,Marco Carraro,Giovanni Minervini,Silvio C.E. Tosatto,Philippe Le Mercier, SARS-CoV-2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion, The Febs Journal, Volume289, Issue14 (2022).
  • Diego Javier Zea, Juan Mac Donagh, Guillermo Benitez, Cristian Guisande Donadio, Julia Marchetti, Nicolas Palopoli, María Silvina Fornasari, Gustavo Parisi, Evolutionary rates in human amyloid proteins reveal their intrinsic metastability, bioRxiv (2022).
  • Clementel D, Del Conte A, Monzon AM, Camagni GF, Minervini G, Piovesan D, Tosatto SCE., RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles, Nucleic Acids Research, Volume 50, Issue W1, Pages W651–W656 (2022).
  • Kumar M, Michael S, Alvarado-Valverde J, Mészáros B, Sámano-Sánchez H, Zeke A, Dobson L, Lazar T, Örd M, Nagpal A, Farahi N, Käser M, Kraleti R, Davey NE, Pancsa R, Chemes LB, Gibson TJ. , The Eukaryotic Linear Motif resource: 2022 release, Nucleic Acids Research, Volume 50, Issue D1, Pages D497–D508 (2022).
  • 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, ECO: the Evidence and Conclusion Ontology, an update for 2022, ucleic Acids Research, Volume 50, Issue D1, Pages D1515–D1521 (2022).
  • Mier, Pablo; Elena-Real, Carlos A; Cortés, Juan; Bernadó, Pau; Andrade-Navarro, Miguel A, The sequence context in poly-alanine regions: structure, function and conservation., Bioinformatics, Volume 38, Issue 21, Pages 4851–4858 (2022).
  • 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, Impact of protein conformational diversity on AlphaFold predictions , Bioinformatics, Volume 38, Issue 10, Pages 2742–2748 (2022).
  • Damiano Piovesan, Alexander Miguel Monzon, Silvio C. E. Tosatto, Intrinsic protein disorder and conditional folding in AlphaFoldDB, Protein Sicence, Volume31, Issue11 (2022).
  • Quaglia, Federicaa;Balakrishnan, Ramac;Bello, Susan M.d;Vasilevsky, Nicole, Conference report: Biocuration 2021 Virtual Conference, Database, Volume 2022 (2022).
  • Bevilacqua, Martina; Paladin, Lisanna; Tosatto, Silvio C E; Piovesan, Damiano, ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications., Bioinformatics, Volume 38, Issue 4, Pages 1129–1130 (2022).
  • Quaglia F, Mészáros B, Salladini E, et al., DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation., Nucleic Acids Res. 2022;50(D1):D480-D487. (2022).
  • Damiano Piovesan, Alexander Miguel Monzon, Federica Quaglia, Silvio C E Tosatto,, Databases for intrinsically disordered proteins, Acta Crystallogr D Struct Biol. Feb 1;78(Pt 2):144-151 (2022).
  • Gustavo Parisi, Nicolas Palopoli, Silvio C.E. Tosatto, María Silvina Fornasari, Peter Tompa, “Protein” no longer means what it used to, Current Research in Structural Biology, Volume 3, Pages 146-152 (2021).
  • Andras Hatos, Alexander Miguel Monzon, Silvio C E Tosatto, Damiano Piovesan, Monika Fuxreiter, FuzDB: a new phase in understanding fuzzy interactions, Nucleic Acids Research (2021).
  • Tamas Lazar et al., PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D404–D411, (2021).
  • Federica Quaglia, Tamas Lazar, András Hatos, Peter Tompa, Damiano Piovesan, Silvio C. E. Tosatto,, Exploring Curated Conformational Ensembles of Intrinsically Disordered Proteins in the Protein Ensemble Database, Current Protocols (2021).
  • Ian Walsh, Dmytro Fishman, Dario Garcia-Gasulla, Tiina Titma, Gianluca Pollastri, ELIXIR Machine Learning Focus Group, Jennifer Harrow, Fotis E. Psomopoulos, Silvio C. E. Tosatto, DOME: recommendations for supervised machine learning validation in biology, Nature Methods (2021).
  • András Hatos, Federica Quaglia, Damiano Piovesan, Silvio C E Tosatto,, APICURON: a database to credit and acknowledge the work of biocurators, Database, Volume 2021, (2021).
  • Marco Necci, Damiano Piovesan, CAID Predictors, DisProt Curators, Silvio C. E. Tosatto, Critical assessment of protein intrinsic disorder prediction, Nature Methods (2021).
  • Alexander Miguel Monzon, Paolo Bonato, Marco Necci, Silvio C.E. Tosatto, Damiano Piovesan, FLIPPER: predicting and characterizing linear interacting peptides in the Protein Data Bank, Journal of Molecular Biology, 166900 (2021).
  • Bálint Mészáros, Hugo Sámano-Sánchez, Jesús Alvarado-Valverde, Jelena Čalyševa, Elizabeth Martínez-Pérez, Renato Alves, Denis C. Shields, Manjeet Kumar, Friedrich Rippmann, Lucía B. Chemes, and Toby J. Gibson, Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications, Science Signaling Vol. 14, Issue 665, eabd0334 (2021).
  • Marco Necci, Damiano Piovesan, Damiano Clementel, Zsuzsanna Dosztányi, Silvio C E Tosatto, MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins, Bioinformatics, Volume 36, Issue 22-23, Pages 5533–5534 (2020).
  • Paladin, Lisanna; Schaeffer, Mathieu; Gaudet, Pascale; Zahn-Zabal, Monique; Michel, Pierre-André; Piovesan, Damiano; Tosatto, Silvio C E; Bairoch, Amos, The Feature-Viewer: a visualization tool for positional annotations on a sequence., Bioinformatics, Volume 36, Issue 10, Pages 3244–3245, (2020).
  • Javier Alonso Iserte, Tamas Lazar, Silvio CE Tosatto, Peter Tompa, Cristina Marino-Buslje, Chasing coevolutionary signals in intrinsically disordered proteins complexes, Scientific Reports volume 10, 17962 (2020).
  • Marco Necci, Damiano Piovesan, Damiano Clementel, Zsuzsanna Dosztányi, Silvio C E Tosatto, MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavours in proteins, Bioinformatics, , btaa1045 (2020).
  • Nicolás Palopoli, Julia Marchetti, Alexander Miguel Monzon, Diego J. Zea, Silvio C. E. Tosatto, María Silvina Fornasari, Gustavo Parisi, Intrinsically disordered protein ensembles shape evolutionary rates revealing conformational patterns, Journal of Molecular Biology, 2020.166751 (2020).
  • 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, MobiDB: intrinsically disordered proteins in 2021, Nucleic Acids Research, gkaa1058 (2020).
  • Federica Quaglia András Hatos Damiano Piovesan Silvio C. E. Tosatto, Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt, Current Protocols in Bioinformatics, Volume 72, Issue 1 (2020).
  • Manjeet Kumar, Marc Gouw, Sushama Michael, Hugo Sámano-Sánchez, Rita Pancsa, Juliana Glavina, Athina Diakogianni, Jesús Alvarado Valverde, Dayana Bukirova, Jelena Čalyševa, Nicolas Palopoli, Norman E Davey, Lucía B Chemes, Toby J Gibson, ELM—the eukaryotic linear motif resource in 2020, Nucleic Acids Research, Volume 48, Issue D1 (2020).
  • Alexander Miguel Monzon, Marco Necci, Federica Quaglia, Ian Walsh, Giuseppe Zanotti, Damiano Piovesan, Silvio C. E. Tosatto, Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank, Int. J. Mol. Sci. 21(12), 4496 (2020).
  • Damiano Piovesan, Andras Hatos, Giovanni Minervini, Federica Quaglia, Alexander Miguel Monzon, Silvio C. E. Tosatto, Assessing predictors for new post translational modification sites: A case study on hydroxylation, PLOS Computational Biology 16(6): e1007967 (2020).
  • Gábor Erdős, Zsuzsanna Dosztányi, Analyzing Protein Disorder with IUPred2A, Current Protocols in Bioinformatics, 70, e99 (2020).
  • Nicolás Palopoli, Javier A. Iserte, Lucia B. Chemes, Cristina Marino-Buslje, Gustavo Parisi, Toby J. Gibson, Norman E. Davey, The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification , Database, Volume 2020, 2020, baaa040 (2020).
  • Patryk Jarnot, Joanna Ziemska-Legiecka, Laszlo 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, PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins, Nucleic Acids Research, Volume 48, Issue W1, Pages W77–W84 (2020).
  • Tadeo E. Saldaño, Victor M. Freixas, Silvio C. E. Tosatto, Gustavo Parisi, and Sebastian Fernandez-Alberti, Exploring Conformational Space with Thermal Fluctuations Obtained by Normal-Mode Analysis, J. Chem. Inf. Model. 2020, 60, 6, 3068–3080 (2020).
  • Kevin T. O’Brien, Catherine Mooney, Cyril Lopez, Gianluca Pollastri and Denis C. Shields, Prediction of polyproline II secondary structure propensity in proteins, R. Soc. open sci. 7: 191239 (2020).
  • 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, PhaSePro: the database of proteins driving liquid–liquid phase separation, Nucleic Acids Research, Volume 48, Issue D1, Pages D360–D367 (2020).
  • András Hatos et al., DisProt: intrinsic protein disorder annotation in 2020, Nucleic Acids Research, Volume 48, Issue D1, Pages D269–D276 (2020).
  • 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, Disentangling the complexity of low complexity proteins, Briefings in Bioinformatics, Volume 21, Issue 2, March 2020, Pages 458-472 (2020).
  • Norman E. Davey, M. Madan Babu, Martin Blackledge et al., An intrinsically disordered proteins community for ELIXIR [version 1; peer review: 2 approved], F1000Research 8(ELIXIR):1753 (2019).
  • Damiano Piovesan, Silvio C E Tosatto, INGA 2.0: improving protein function prediction for the dark proteome, Nucleic Acids Research, Volume 47, Issue W1 (2019).
  • Julia Marchetti, Alexander Miguel Monzon, Silvio C.E.Tosatto, Gustavo Parisi, María Silvina Fornasari, Ensembles from Ordered and Disordered Proteins Reveal Similar Structural Constraints during Evolution, Journal of Molecular Biology, Volume 431, Issue 6, 15 March 2019, Pages 1298-1307 (2019).
  • Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist et al., The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens, Genome Biology volume 20, Article number: 244 (2019).
  • Marco Necci, Damiano Piovesan, Silvio C E Tosatto, Where differences resemble: sequence-feature analysis in curated databases of intrinsically disordered proteins, Database, Volume 2018 (2018).

Resources

  • Flipper (D1.5) [private]: Fast Linear Interacting Peptides PrEdictoR A sequence based predictor of LIPS, i.e. regions or residues that interact with other proteins or DNA/RNA preserving a linear (disordered) structure. Flipper is a neural network trained on latest DisProt data that identifies LIPS from sequence.
  • DisProt homology transfer (D1.4) [private]: An algorithm to extend DisProt annotation to homologous genes. DisProt contains high quality annotations of protein intrinsic disorder obtained through manual curation. Evidence of disorder is often found for some organisms (usually model organisms), but missing for others. While it could be tempting to extend annotation by simple sequence similarity, it has been shown that even one single residue can cause a protein to completely fold or unfold. This algorythm is specifically designed to assess the transferability of disorder annotation to homologous proteins.
  • PED automatic extraction (D1.1) [private]: The goal of PED is to serve as an openly accessible database for the deposition of structural ensembles of IDPs and of denatured proteins based on nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and other data measured in solution. This software automatically generates PED entries from ensemble data
  • IDPOntology (D2.1) [private]: Ontology of intrinsically disordered proteins in OWL and OBO formats. Currently at its 0.1.0 version. Used in DisProt 8.0+
  • Pubmederman (D1.3) [private]: software to search PPI interactions from annotations in scientific publications in order to be presented to database curators like DisProt. Pubmederman uses information from Uniprot, Pfam, Scilite, Hippie and PDB.