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Repeat protein Function Refinement, Annotation and Classification of Topologies

Deliverables

Collection of TRP datasets.

Collection of TRP datasets

Report on the state-of-the-art of TRP-related HMMs and TRP covariance analysis.
Report on the function of new TRP families.

Report on the function of new TRP families

Report on examples of TRP evolution through internal duplication of coding sequence and repeat units recycled by evolution in globular structures.

Report on examples of TRP evolution through internal duplication of coding sequence and repeat units recycled by evolution in globular structures

Report on mapping and analysis of exon boundaries on TRPs, comparison with their modularity, and TRP amino acid vs DNA sequence variability.

Report on mapping and analysis of exon boundaries on TRPs comparison with their modularity and TRP amino acid vs DNA sequence variability

TRP function, localization and organism distribution enrichment analysis.

TRP function localization and organism distribution enrichment analysis

Symposia/Remote Symposia Period 1

Symposia Period 1 Europe 2 x AllHands Meeting 1 x Dissemination Training School Latin America 2 x Annual Latin America Visit

Report about TRP roles in PPI networks and interaction with RNA/DNA molecules and role of TRPs in host interactions with viruses and pathogens.

Report about TRP roles in PPI networks and interaction with RNADNA molecules and role of TRPs in host interactions with viruses and pathogens

Report on TRP disorder, low-complexity, transmembrane domain overlap and examples of cooperative TRP folding.

Report on TRP disorder lowcomplexity transmembrane domain overlap and examples of cooperative TRP folding

Cookbook for TRP annotation best-practices. Report about data format gold-standard, technical and implementation best-practices for TRP web resources.

Cookbook for TRP annotation bestpractices Report about data format goldstandard technical and implementation bestpractices for TRP web resources

Report on SLIMs in TRPs.

Report on SLIMs in TRPs

Publications

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 8, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa055

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

A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder

Author(s): Matteo Delucchi, Elke Schaper, Oxana Sachenkova, Arne Elofsson and Maria Anisimova
Published in: Genes, 2020, ISSN 2073-4425
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes11040407

"""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 8, 2021, ISSN 2665-928X
Publisher: Elsevier
DOI: 10.1016/j.crstbi.2021.06.002

DOME: recommendations for supervised machine learning validation in biology

Author(s): 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
Published in: Nature Methods, 2021, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-021-01205-4

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; Giuseppe Zanotti; Damiano Piovesan; Silvio C. E. Tosatto
Published in: International Journal of Molecular Sciences, Issue 8, 2020, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.1101/2020.02.17.952028

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

Author(s): Damiano Clementel, Alessio Del Conte, Alexander Miguel Monzon, Giorgia F Camagni, Giovanni Minervini, Damiano Piovesan, Silvio C E Tosatto
Published in: Nucleic Acids Research, 2022, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac365

Tally-2.0: upgraded validator of tandem repeat detection in protein sequences.

Author(s): Vladimir Perovic; Jeremy Y Leclercq; Neven Sumonja; Francois Richard; Francois Richard; Nevena Veljkovic; Andrey V. Kajava
Published in: Bioinformatics, Issue 8, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa121

RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures.

Author(s): Lisanna Paladin; Martina Bevilacqua; Sara Errigo; Damiano Piovesan; Ivan Mičetić; Marco Necci; Alexander Miguel Monzon; María Laura Fabre; José Luis López; Juliet F. Nilsson; Javier Rios; Pablo Lorenzano Menna; Maia Diana Eliana Cabrera; Martin Gonzalez Buitron; Mariane Gonçalves Kulik; Sebastian Fernandez-Alberti; María Silvina Fornasari; Gustavo Parisi; Antonio Lagares; Layla Hirsh; Migue
Published in: Nucleic Acids Research, Issue 4, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa1097

Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families

Author(s): Claudio Bassot, Arne Elofsson
Published in: PLOS Computational Biology, 2021, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1008798

A novel approach to investigate the evolution of structured tandem repeat protein families by exon duplication

Author(s): Lisanna Paladin, Marco Necci, Damiano Piovesan, Pablo Mier, Miguel A.Andrade-Navarro, Silvio C.E.Tosatto
Published in: Journal of Structural Biology, 2022, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2020.107608

Beyond Microsatellite Instability: Intrinsic Disorder as a Potential Link Between Protein Short Tandem Repeats and Cancer

Author(s): Max A. Verbiest, Matteo Delucchi, Tugce Bilgin Sonay and Maria Anisimova
Published in: Frontiers in Bioinformatics, 2021, ISSN 2673-7647
Publisher: Frontiers Media
DOI: 10.3389/fbinf.2021.685844

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

The features of polyglutamine regions depend on their evolutionary stability

Author(s): Pablo Mier, Miguel A. Andrade-Navarro
Published in: BMC Ecology and Evolution, 2020, ISSN 2730-7182
Publisher: Springer Nature
DOI: 10.1186/s12862-020-01626-3

REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences

Author(s): Mohamed Kamel, Kristina Kastano, Pablo Mier, Miguel A. Andrade
Published in: Journal of Molecular Biology, 2021, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2021.166895

TRAL 2.0 : tandem repeat detection with circular profile hidden Markov models and evolutionary aligner

Author(s): Matteo Delucchi; Paulina Näf; Spencer Bliven; Maria Anisimova
Published in: Frontiers in Bioinformatics, Issue 5, 2021, ISSN 2673-7647
Publisher: Frontiers Media
DOI: 10.21256/zhaw-22764

Pfam: The protein families database in 2021.

Author(s): Jaina Mistry; Sara Chuguransky; Lowri Williams; Matloob Qureshi; Gustavo A. Salazar; Erik L. L. Sonnhammer; Silvio C. E. Tosatto; Lisanna Paladin; Shriya Raj; Lorna Richardson; Robert D. Finn; Alex Bateman
Published in: Nucleic Acids Research, Issue 5, 2020, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa913

Conference report: Biocuration 2021 Virtual Conference

Author(s): Federica Quaglia, Rama Balakrishnan, Susan M Bello, Nicole Vasilevsky
Published in: Database, 2022, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/baac027

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 7, 2020, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa339

14th Annual Biocuration Conference (virtual) - Abstracts from the invited speakers talks and poster session presentations

Author(s): Federica Quaglia
Published in: Abstract booklet of the 14th Annual Biocuration Conference (virtual), including invited speakers talks and poster session presentations, 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5570276

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

Author(s): Nahuel Escobedo, Ronaldo Romario Tunque Cahui, Gastón Caruso, Emilio García Ríos, Layla Hirsh, Alexander Miguel Monzon, Gustavo Parisi, VNicolas Palopoli
Published in: bioRxiv, 2022, ISSN 2692-8205
Publisher: bioRxiv
DOI: 10.1101/2022.02.15.480082

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