H2020 MSCA-RISE project

EU funding acknowledgement

How to acknowledge REFRACT

REFRACT must acknowledge the support of the European Union in all its activities, related publications, and/or other media. All results, publications, scientific and communication outputs shall inform on EU funding with the following statement, possibly accompanied by the EU logo:

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 823886.

Publications

  • Pablo Mier, Miguel A. Andrade-Navarro, The features of polyglutamine regions depend on their evolutionary stability, BMC Evolutionary Biology , Volume 20, Article number: 59 (2020). Go to article→
  • Lisanna Paladin, Martina Bevilacqua, Sara Errigo, Damiano Piovesan, Ivan Mičetić, Marco Necci, Alexander Miguel Monzon, Maria Laura Fabre, Jose Luis Lopez, Juliet F Nilsson, Javier Rios, Pablo Lorenzano Menna, Maia Cabrera, Martin Gonzalez Buitron, Mariane Gonçalves Kulik, Sebastian Fernandez-Alberti, Maria Silvina Fornasari, Gustavo Parisi, Antonio Lagares, Layla Hirsh, Miguel A Andrade-Navarro, Andrey V Kajava, Silvio C E Tosatto, RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures, Nucleic Acids Research , gkaa1097 (2020). Go to article→
  • Lisanna Paladin, Marco Necci, Damiano Piovesan, Pablo Mier, Miguel A. Andrade-Navarro, Silvio C.E. Tosatto, A novel approach to investigate the evolution of structured tandem repeat protein families by exon duplication, Journal of Structural Biology , Vol 212, Iss 2, 107608 (2020). Go to article→
  • Alexander M. 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, International Journal of Molecular Sciences , Vol 21, Iss 12, page 4496 (2020). Go to article→
  • 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 , Vol 48, Iss W1, Pages W77-W84 (2020). Go to article→
  • Vladimir Perovic, Jeremy Y. Leclercq, Neven Sumonja, Francois D. Richard, Nevena Veljkovic, Andrey V. Kajava, Tally-2.0: upgraded validator of tandem repeat detection in protein sequences, Bioinformatics , Vol 36, Iss 10, Pages 3260–3262 (2020). Go to article→
  • Matteon Delucchi, Elke Schaper, Oxana Sachenkova, Arne Elofsson, Maria Anisimova, A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder, Genes , 11, no. 4: 407 (2020). Go to article→
  • Lisanna Paladin, Mathieu Schaeffer, Pascale Gaudet, Monique Zahn-Zabal, Pierre-André Michel, Damiano Piovesan, Silvio C.E. Tosatto, Amos Bairoch, The Feature-Viewer: a visualization tool for positional annotations on a sequence, Bioinformatics , Vol 36, Iss 10, Pages 3244–3245 (2020). Go to article→
  • Mohamed Kamel, Kristina Kastano, Pablo Mier, Miguel A. Andrade, REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences, Journal of Molecular Biology , Volume 433, Issue 11, 166895 (2021). Go to article→
  • Martina Bevilacqua, Lisanna Paladin, Silvio C E Tosatto, Damiano Piovesan, 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 (2021). Go to article→
  • 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 , Volume 18, Pages 1122–1127 (2021). Go to article→
  • András Hatos, Federica Quaglia, Damiano Piovesan, Silvio C E Tosatto, APICURON: a database to credit and acknowledge the work of biocurators, Database , Volume 2021, baab019 (2021). Go to article→
  • Federica Quaglia, “14th Annual Biocuration Conference (virtual) - Abstracts from the invited speakers talks and poster session presentations, International Society for Biocuration , Publisher: Zenodo (2021). Go to article→
  • Gustavo Parisi, Nicolas Palopoli, Silvio C.E.Tosatto, María Silvina Fornasari, PeterTompa, Protein” no longer means what it used to, Current Research in Structural Biology , Volume 3, Pages 146-152 (2021). Go to article→
  • Jaina Mistry, Sara Chuguransky, Lowri Williams, Matloob Qureshi, Gustavo A Salazar, Erik L L Sonnhammer, Silvio C E Tosatto, Lisanna Paladin, Shriya Raj, Lorna J Richardson, Robert D Finn, Alex Bateman, Pfam: The protein families database in 2021 , Nucleic Acids Research , Volume 49, Issue D1, Pages D412–D419 (2021). Go to article→
  • Max A. Verbiest, Matteo Delucchi, Tugce Bilgin Sonay, Maria Anisimova, Beyond Microsatellite Instability: Intrinsic Disorder as a Potential Link Between Protein Short Tandem Repeats and Cancer, Frontiers in Bioinformatics , vol. 1 fbinf.2021.685844 (2021). Go to article→
  • Matteo Delucchi, Paulina Näf, Spencer Bliven, Maria Anisimova, TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner, Frontiers in Bioinformatics , 17(4):e1008798 (2021). Go to article→
  • Claudio Bassot, Arne Elofsson, Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families, PL9S Computational Biology , 17(4):e1008798 (2021). Go to article→
  • Osmanli Z.; Falgarone T.; Samadova T.; Aldrian G.; Leclercq J.; Shahmuradov I.; Kajava A.V., The Difference in Structural States between Canonical Proteins and Their Isoforms Established by Proteome-Wide Bioinformatics Analysis, Biomolecules , Volume 12(11), 1610 (2022). Go to article→
  • Mier P.; Elena-Real C.A.; Cortés J.; Bernadó P.; Andrade-Navarro M.A., The sequence context in poly-alanine regions: structure, function and conservation, Bioinformatics , Volume 38, Issue 21, Pages 4851–4858 (2022). Go to article→
  • Damiano Clementel, Alessio Del Conte, Alexander Miguel Monzon, Giorgia F Camagni, Giovanni Minervini, Damiano Piovesan, Silvio C E Tosatto, RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles, Nucleic Acids Research , Volume 50, Issue W1, Pages W651–W656 (2022). Go to article→
  • Federica Quaglia, Rama Balakrishnan, Susan M Bello, Nicole Vasilevsky, Conference report: Biocuration 2021 Virtual Conference , Database , Volume 2022 (2022). Go to article→
  • Nahuel Escobedo, Ronaldo Romario Tunque Cahui, Gastón Caruso, Emilio García Ríos, Layla Hirsh, Alexander Miguel Monzon, Gustavo Parisi, VNicolas Palopoli, CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure, Bioinformatics , Volume 38, Issue 21, Pages 4959–4961 (2022). Go to article→
  • Falgarone T.; Villain E.; Richard F.; Osmanli Z.; Kajava A.V., Census of exposed aggregation-prone regions in proteomes, Briefings in Bioinformatics , Volume 24, Issue 4 (2023). Go to article→
  • Verbiest M.; Maksimov M.; Jin Y.; Anisimova M.; Gymrek M.; Bilgin Sonay T., Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species, Journal of Evolutionary Biology , Volume 36, Issue 2, Pages 321–336 (2023). Go to article→
  • Monzon A.M.; Arrías P.N.; Elofsson A.; Mier P.; Andrade-Navarro M.A.; Bevilacqua M.; Clementel D.; Bateman A.; Hirsh L.; Fornasari M.S.; Parisi G.; Piovesan D.; Kajava A.V.; Tosatto S.C.E., A STRP-ed definition of Structured Tandem Repeats in Proteins, Journal of Structural Biology , Volume 215, Issue 4, December 2023, 108023 (2023). Go to article→
  • Manasra S.; Kajava A.V., Why does the first protein repeat often become the only one?, Journal of Structural Biology , Volume 215, Issue 3, 108014 (2023). Go to article→
  • Lundström O.S.; Adriaan Verbiest M.; Xia F.; Jam H.Z.; Zlobec I.; Anisimova M.; Gymrek M., WebSTR: A Population-wide Database of Short Tandem Repeat Variation in Humans, Journal of Molecular Biology , Volume 435, Issue 20, 168260 (2023). Go to article→
  • Ferrelli M.L.; Pidre M.L.; García-Domínguez R.; Alberca L.N.; del Saz-Navarro D.M.; Santana-Molina C.; Devos D.P., Prokaryotic membrane coat - like proteins: An update, Journal of Structural Biology , Volume 215, Issue 3, 107987 (2023). Go to article→
  • Escobedo N.; Monzon A.M.; Fornasari M.S.; Palopoli N.; Parisi G., Combining Protein Conformational Diversity and Phylogenetic Information Using CoDNaS and CoDNaS-Q, Current Protocols , Volume 3 (2023). Go to article→
  • Erdozain S.; Barrionuevo E.; Ripoll L.; Mier P.; Andrade-Navarro M.A., Protein repeats evolve and emerge in giant viruses, Journal of Structural Biology , Volume 215, Issue 2, June 2023, 107962 (2023). Go to article→
  • Elena-Real C.A.; Mier P.; Sibille N.; Andrade-Navarro M.A.; Bernadó P., Structure–function relationships in protein homorepeats, Current Opinion in Structural Biology , Volume 83, December 2023, 102726 (2023). Go to article→
  • Del Conte A.; Monzon A.M.; Clementel D.; Camagni G.F.; Minervini G.; Tosatto S.C.E.; Piovesan D., RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics, Bioinformatics , Bioinformatics, Volume 39, Issue 5 (2023). Go to article→
  • Del Conte A.; Bouhraoua A.; Mehdiabadi M.; Clementel D.; Monzon A.M.; Tosatto S.C.E.; Piovesan D.; Holehouse A.S.; Griffith D.; Emenecker R.J.; Patil A.; Sharma R.; Tsunoda T.; Sharma A.; Tang Y.J.; Liu B.; Mirabello C.; Wallner B.; Rost B.; Ilzhöfer D.; Littmann M.; Heinzinger M.; Krautheimer L.I.M.; Bernhofer M.; McGuffin L.J.; Callebaut I.; Feildel T.B.; Liu J.; Cheng J.; Guo Z.; Xu J.; Wang S.; Malhis N.; Gsponer J.; Kim C.-S.; Han K.-S.; Ma M.-C.; Kurgan L.; Ghadermarzi S.; Katuwawala A.; Zhao B.; Peng Z.; Wu Z.; Hu G.; Wang K.; Hoque M.T.; Ul Kabir M.W.; Vendruscolo M.; Sormanni P.; Li M.; Zhang F.; Jia P.; Wang Y.; Lobanov M.Y.; Galzitskaya O.V.; Vranken W.; Díaz A.; Litfin T.; Zhou Y.; Hanson J.; Paliwal K.; Dosztányi Z.; Erdős G., CAID prediction portal: A comprehensive service for predicting intrinsic disorder and binding regions in proteins, Nucleic Acids Research , Volume 51, Issue W1, Pages W62–W69 (2023). Go to article→
  • Conte A.D.; Mehdiabadi M.; Bouhraoua A.; Mozon A.M.; Tosatto S.C.E.; Piovesan D., Critical assessment of protein intrinsic disorder prediction (CAID) - Results of round 2, Proteins , Volume 91, Issue 12 (2023). Go to article→
  • Bezerra-Brandao M.; Tunque Cahui R.R.; Hirsh L., Daisy: An integrated repeat protein curation service, Journal of Structural Biology , Volume 215, Issue 4, December 2023, 108033 (2023). Go to article→
  • Arrías P.N.; Monzon A.M.; Clementel D.; Mozaffari S.; Piovesan D.; Kajava A.V.; Tosatto S.C.E., The repetitive structure of DNA clamps: An overlooked protein tandem repeat, Journal of Structural Biology , Volume 215, Issue 3, 108001 (2023). Go to article→
  • Mac Donagh J.; Marchesini A.; Spiga A.; Fallico M.J.; Arrías P.N.; Monzon A.M.; Vagiona A.-C.; Gonçalves-Kulik M.; Mier P.; Andrade-Navarro M.A., Structured Tandem Repeats in Protein Interactions, International Journal of Molecular Sciences , Volume 25(5):2994 (2024). Go to article→
  • Verbiest M.A.; Lundström O.; Xia F.; Baudis M.; Bilgin Sonay T.; Anisimova M., Short tandem repeat mutations regulate gene expression in colorectal cancer, Scientific Reports , Volume 14, Article number: 3331 (2024). Go to article→
  • Ghafouri H.; Lazar T.; Del Conte A.; Tenorio Ku L.G.; Tompa P.; Tosatto S.C.E.; Monzon A.M.; Aspromonte M.C.; Bernadó P.; Chaves-Arquero B.; Chemes L.B.; Clementel D.; Cordeiro T.N.; Elena-Real C.A.; Feig M.; Felli I.C.; Ferrari C.; Forman-Kay J.D.; Gomes T.; Gondelaud F.; Gradinaru C.C.; Ha-Duong T.; Head-Gordon T.; Heidarsson P.O.; Janson G.; Jeschke G.; Leonardi E.; Liu Z.H.; Longhi S.; Lund X.L.; Macias M.J.; Martin-Malpartida P.; Mercadante D.; Mouhand A.; Nagy G.; Nugnes M.V.; Pérez-Cañadillas J.M.; Pesce G.; Pierattelli R.; Piovesan D.; Quaglia F.; Ricard-Blum S.; Robustelli P.; Sagar A.; Salladini E.; Sénicourt L.; Sibille N.; Teixeira J.M.C.; Tsangaris T.E.; Varadi M., PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins, Nucleic Acids Research , Volume 52, Issue D1, Pages D536–D544 (2024). Go to article→
  • Aspromonte M.C.; Nugnes M.V.; Quaglia F.; Bouharoua A.; Tosatto S.C.E.; Piovesan D., DisProt in 2024: improving function annotation of intrinsically disordered proteins, Nucleic Acids Research , Volume 52, Issue D1, 5 January 2024, Pages D434–D441 (2024). Go to article→

Resources

RepeatsDB
a database of annotated tandem repeat protein structures. The database provides unit position, classification and reference to other databases.
Tally 2.0
a scoring tool based on a machine learning approach, which allows to validate the results of tandem repeat detection in protein sequences.
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 823886.