Repeat protein Function Refinement, Annotation and Classification of Topologies

Informations projet

REFRACT

N° de convention de subvention: 823886

DOI

10.3030/823886

Projet clôturé

Date de signature de la CE 26 Octobre 2018

Date de début 1 Janvier 2019

Date de fin 30 Juin 2024

Financé au titre de

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Coût total

€ 2 392 000,00

Contribution de l’UE

€ 2 226 400,00

Coordonné par

UNIVERSITA DEGLI STUDI DI PADOVA
Italy

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

Documents, reports (13)

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

Symposia/Remote Symposia Period 2

Symposia Period 2. Europe: 2 x All-Hands Meeting, 1 x Dissemination Training School, 1 x Final Dissemination meeting. Latin America: 2 x Annual Latin America Visit.

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

Report on TRP sequence and structural classification as well as sequence and structural clustering of the TRP universe.
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

Demonstrators, pilots, prototypes (9)

Software for sequence- and structure-based pairwise TRP alignment

Software for sequence- and structure-based pairwise TRP alignment.

Cross-link of generated TRP data into core data resources (e.g. InterPro) and related resources.
Platform and metrics for TRP tools benchmarking, including consensus detection of sequence- and structure-based methods

Platform and metrics for TRP tools benchmarking, including consensus detection of sequence- and structure-based methods.

Deployment of TRP database APIs.
Software for automatic TRP region and unit annotation
Software for the identification of homologous TRPs from sequence databases.
Integration of novel classification in TRP databases.
Curation of Pfam TRP-related HMMs.
Software for modeling TRP regions by homology

Websites, patent fillings, videos etc. (1)

Online presence (website and social media)

Publications

Peer reviewed articles (41)

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

Auteurs: Lisanna Paladin; Mathieu Schaeffer; Pascale Gaudet; Monique Zahn-Zabal; Pierre-André Michel; Damiano Piovesan; Silvio C. E. Tosatto; Amos Marc Bairoch
Publié dans: Bioinformatics, Numéro 8, 2020, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btaa055

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

Auteurs: Del Conte A.; Monzon A. M.; Clementel D.; Camagni G. F.; Minervini G.; Tosatto S. C. E.; Piovesan D.
Publié dans: Bioinformatics, Numéro 16, 2023, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btad260

Prokaryotic membrane coat - like proteins: An update

Auteurs: M. Leticia Ferrelli; Matías L. Pidre; Ruben García-Domínguez; Lucas N. Alberca; DMaría del Saz-Navarro; Carlos Santana-Molina; Damien P. Devos
Publié dans: Journal of Structural Biology, Numéro 8, 2023, ISSN 1047-8477
Éditeur: Academic Press
DOI: 10.1016/j.jsb.2023.107987

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

Auteurs: Martina Bevilacqua, Lisanna Paladin, Silvio C E Tosatto, Damiano Piovesan
Publié dans: Bioinformatics, 2021, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btab764

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

Auteurs: Matteo Delucchi, Elke Schaper, Oxana Sachenkova, Arne Elofsson and Maria Anisimova
Publié dans: Genes, 2020, ISSN 2073-4425
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes11040407

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

Auteurs: Pablo Mier, Carlos A Elena-Real, Juan Cortés, Pau Bernadó, Miguel A Andrade-Navarro
Publié dans: Bioinformatics, 2022, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btac610

The nucleotide landscape of polyXY regions

Auteurs: Pablo Mier, Miguel A. Andrade-Navarro
Publié dans: Computational and Structural Biotechnology Journal, Numéro 21, 2024, Page(s) 5408-5412, ISSN 2001-0370
Éditeur: Elsevier
DOI: 10.1016/j.csbj.2023.10.054

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

Auteurs: Gustavo Parisi; Nicolas Palopoli; Silvio C. E. Tosatto; María Silvina Fornasari; Peter Tompa
Publié dans: Current Research in Structural Biology, Numéro 8, 2021, ISSN 2665-928X
Éditeur: Elsevier
DOI: 10.1016/j.crstbi.2021.06.002

WebSTR: A Population-wide Database of Short Tandem Repeat Variation in Humans

Auteurs: Lundström OS, Adriaan Verbiest M, Xia F, Jam HZ, Zlobec I, Anisimova M, Gymrek M
Publié dans: Journal of Molecular Biology, 2023, ISSN 0022-2836
Éditeur: Academic Press
DOI: 10.1016/j.jmb.2023.168260

DOME: recommendations for supervised machine learning validation in biology

Auteurs: 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
Publié dans: Nature Methods, 2021, ISSN 1548-7091
Éditeur: 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

Auteurs: Alexander Miguel Monzon; Marco Necci; Federica Quaglia; Ian Walsh; Giuseppe Zanotti; Damiano Piovesan; Silvio C. E. Tosatto
Publié dans: International Journal of Molecular Sciences, Numéro 8, 2020, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.1101/2020.02.17.952028

Census of exposed aggregation-prone regions in proteomes

Auteurs: Théo Falgarone, Etienne Villain, Francois Richard, Zarifa Osmanli, Andrey V Kajava
Publié dans: Briefings in Bioinformatics, 2023, ISSN 1467-5463
Éditeur: Oxford University Press
DOI: 10.1093/bib/bbad183

The repetitive structure of DNA clamps: An overlooked protein tandem repeat

Auteurs: Arrías PN, Monzon AM, Clementel D, Mozaffari S, Piovesan D, Kajava AV, Tosatto SCE
Publié dans: Journal of Structural Biology, 2023, ISSN 1047-8477
Éditeur: Academic Press
DOI: 10.1016/j.jsb.2023.108001

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

Auteurs: Damiano Clementel, Alessio Del Conte, Alexander Miguel Monzon, Giorgia F Camagni, Giovanni Minervini, Damiano Piovesan, Silvio C E Tosatto
Publié dans: Nucleic Acids Research, 2022, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkac365

Daisy: An integrated repeat protein curation service

Auteurs: Manuel, Bezerra-Brandao; Ronaldo Romario, Tunque Cahui; Layla, Hirsh
Publié dans: Journal of Structural Biology, Numéro 6, 2023, ISSN 1047-8477
Éditeur: Academic Press
DOI: 10.1016/j.jsb.2023.108033

Structured Tandem Repeats in Protein Interactions

Auteurs: Mac Donagh J, Marchesini A, Spiga A, Fallico MJ, Arrías PN, Monzon AM, Vagiona AC, Gonçalves-Kulik M, Mier P, Andrade-Navarro MA
Publié dans: International Journal of Molecular Sciences, 2024, ISSN 1661-6596
Éditeur: Multidisciplinary Digital Publishing Institute
DOI: 10.3390/ijms25052994

CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods

Auteurs: Piovesan, Damiano; Zago, Davide; Joshi, Parnal; Kaluza, M. Clara De Paolis; Monzon, Alexander Miguel; Reade, Walter; Friedberg, Iddo; Radivojac, Predrag; Tosatto, Silvio C. E.
Publié dans: Bioinformatics Advances, Numéro 16, 2024, ISSN 2635-0041
Éditeur: Oxford University Press
DOI: 10.1093/bioadv/vbae043

Structure-function relationships in protein homorepeats

Auteurs: Elena-Real CA, Mier P, Sibille N, Andrade-Navarro MA, Bernadó P.
Publié dans: Current Opinion in Structural Biology, 2023, ISSN 0959-440X
Éditeur: Elsevier BV
DOI: 10.1016/j.sbi.2023.102726

Protein repeats evolve and emerge in giant viruses

Auteurs: Erdozain Bagolin, Sofía Agostina; Barrionuevo, Emilia Mercedes; Ripoll, Lucas; Mier, Pablo; Andrade Navarro, Miguel A.
Publié dans: Journal of Structural Biology, Numéro 11, 2023, ISSN 1047-8477
Éditeur: Academic Press
DOI: 10.1016/j.jsb.2023.107962

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

Auteurs: Vladimir Perovic; Jeremy Y Leclercq; Neven Sumonja; Francois Richard; Francois Richard; Nevena Veljkovic; Andrey V. Kajava
Publié dans: Bioinformatics, Numéro 8, 2020, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btaa121

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

Auteurs: Escobedo N, Monzon AM, Fornasari MS, Palopoli N, Parisi G
Publié dans: Current Protocols, 2023, ISSN 2691-1299
Éditeur: John Wiley & Sons
DOI: 10.1002/cpz1.764

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

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 4, 2021, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkaa1097

Why does the first protein repeat often become the only one?

Auteurs: Manasra S, Kajava AV
Publié dans: Journal of Structural Biology, 2023, ISSN 1047-8477
Éditeur: Academic Press
DOI: 10.1016/j.jsb.2023.108014

Critical assessment of protein intrinsic disorder prediction (<scp>CAID</scp>) ‐ Results of round 2

Auteurs: Del Conte A.; Mehdiabadi M.; Bouhraoua A.; Monzon A. M.; Tosatto S. C. E.; Piovesan D.
Publié dans: Proteins: Structure, Function and Bioinformatics, Numéro 15, 2023, ISSN 0887-3585
Éditeur: Wiley-Liss Inc
DOI: 10.1002/prot.26582

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

Auteurs: Claudio Bassot, Arne Elofsson
Publié dans: PLOS Computational Biology, 2021, ISSN 1553-734X
Éditeur: Public Library of Science
DOI: 10.1371/journal.pcbi.1008798

Expanding the repertoire of human tandem repeat RNA-binding proteins

Auteurs: Agustín Ormazábal; Matías Sebastián Carletti; Tadeo Enrique Saldaño; Martín Gonzalez-Buitron; Julia Marchetti; Nicolas Palopoli; Alex Bateman
Publié dans: PLoS ONE, Numéro 11, 2023, ISSN 1932-6203
Éditeur: Public Library of Science
DOI: 10.1371/journal.pone.0290890

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

Auteurs: Lisanna Paladin, Marco Necci, Damiano Piovesan, Pablo Mier, Miguel A.Andrade-Navarro, Silvio C.E.Tosatto
Publié dans: Journal of Structural Biology, 2022, ISSN 1047-8477
Éditeur: Academic Press
DOI: 10.1016/j.jsb.2020.107608

Short tandem repeat mutations regulate gene expression in colorectal cancer

Auteurs: Max A. Verbiest; Oxana Lundström; Feifei Xia; Michael Baudis; Tugce Bilgin Sonay; Maria Anisimova
Publié dans: Scientific Reports, Numéro 18, 2024, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1101/2023.11.29.569189

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

Auteurs: Max A. Verbiest, Matteo Delucchi, Tugce Bilgin Sonay and Maria Anisimova
Publié dans: Frontiers in Bioinformatics, 2021, ISSN 2673-7647
Éditeur: Frontiers Media
DOI: 10.3389/fbinf.2021.685844

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

Auteurs: András Hatos, Federica Quaglia, Damiano Piovesan, Silvio C E Tosatto
Publié dans: Database, 2021, ISSN 1758-0463
Éditeur: Oxford University Press
DOI: 10.1093/database/baab019

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

Auteurs: Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon, CAID predictors , Silvio C E Tosatto, Damiano Piovesan
Publié dans: Nucleic Acids Research, 2023, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkad430

The features of polyglutamine regions depend on their evolutionary stability

Auteurs: Pablo Mier, Miguel A. Andrade-Navarro
Publié dans: BMC Ecology and Evolution, 2020, ISSN 2730-7182
Éditeur: Springer Nature
DOI: 10.1186/s12862-020-01626-3

The Difference in Structural States between Canonical Proteins and Their Isoforms Established by Proteome-Wide Bioinformatics Analysis

Auteurs: Osmanli, Z.; Falgarone, T.; Samadova, T.; Aldrian, G.; Leclercq, J.; Shahmuradov, I.; Kajava, A.V.
Publié dans: Biomolecules, 2022, ISSN 2218-273X
Éditeur: Multidisciplinary Digital Publishing Institute
DOI: 10.3390/biom12111610

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

Auteurs: Mohamed Kamel, Kristina Kastano, Pablo Mier, Miguel A. Andrade
Publié dans: Journal of Molecular Biology, 2021, ISSN 0022-2836
Éditeur: Academic Press
DOI: 10.1016/j.jmb.2021.166895

PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins

Auteurs: Hamidreza Ghafouri; Tamas Lazar; Alessio Del Conte; Luiggi G Tenorio Ku; Maria C Aspromonte; Pau Bernadó; Belén Chaves-Arquero; Lucia Beatriz Chemes; Damiano Clementel; Tiago N Cordeiro; Carlos A Elena-Real; Michael Feig; Isabella C Felli; Carlo Ferrari; Julie D Forman-Kay; Tiago Gomes; Frank Gondelaud; Claudiu C Gradinaru; Tâp Ha-Duong; Teresa Head-Gordon; Pétur O Heidarsson; Giacomo Janson
Publié dans: Nucleic Acids Research, Numéro 16, 2024, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkad947

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

Auteurs: Matteo Delucchi; Paulina Näf; Spencer Bliven; Maria Anisimova
Publié dans: Frontiers in Bioinformatics, Numéro 5, 2021, ISSN 2673-7647
Éditeur: Frontiers Media
DOI: 10.21256/zhaw-22764

Pfam: The protein families database in 2021.

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 5, 2020, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkaa913

A STRP-ed definition of Structured Tandem Repeats in Proteins

Auteurs: Monzon, Alexander Miguel; Arrías, Paula Nazarena; Elofsson, Arne; Mier, Pablo; Andrade-Navarro, Miguel A; Bevilacqua, Martina; Clementel, Damiano; Bateman, Alex; Hirsh, Layla; Fornasari, Maria Silvina; Parisi, Gustavo; Piovesan, Damiano; Kajava, Andrey V; Tosatto, Silvio C E
Publié dans: Journal of Structural Biology, Numéro 5, 2023, ISSN 1047-8477
Éditeur: Academic Press
DOI: 10.1016/j.jsb.2023.108023

DisProt in 2024: improving function annotation of intrinsically disordered proteins

Auteurs: Maria Cristina Aspromonte; Maria Victoria Nugnes; Federica Quaglia; Adel Bouharoua; Vasileios Sagris; Vasilis J Promponas; Anastasia Chasapi; Erzsébet Fichó; Galo E Balatti; Gustavo Parisi; Martín González Buitrón; Gabor Erdos; Matyas Pajkos; Zsuzsanna Dosztányi; Laszlo Dobson; Alessio Del Conte; Damiano Clementel; Edoardo Salladini; Emanuela Leonardi; Fatemeh Kordevani; Hamidreza Ghafouri;
Publié dans: Nucleic Acids Research, Numéro 18, 2024, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkad928

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

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 7, 2020, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkaa339

Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species

Auteurs: Max Verbiest; Mikhail Maksimov; Ye Jin; Maria Anisimova; Melissa Gymrek; Tugce Bilgin Sonay
Publié dans: Journal of Evolutionary Biology, Numéro 18, 2023, ISSN 1010-061X
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/jeb.14106

Other (1)

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

Auteurs: Federica Quaglia
Publié dans: Abstract booklet of the 14th Annual Biocuration Conference (virtual), including invited speakers talks and poster session presentations, 2021
Éditeur: Zenodo
DOI: 10.5281/zenodo.5570276

Non-peer reviewed articles (1)

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

Auteurs: Nahuel Escobedo, Ronaldo Romario Tunque Cahui, Gastón Caruso, Emilio García Ríos, Layla Hirsh, Alexander Miguel Monzon, Gustavo Parisi, VNicolas Palopoli
Publié dans: bioRxiv, 2022, ISSN 2692-8205
Éditeur: bioRxiv
DOI: 10.1101/2022.02.15.480082

Conference proceedings (1)

Conference report: Biocuration 2021 Virtual Conference

Auteurs: Federica Quaglia, Rama Balakrishnan, Susan M Bello, Nicole Vasilevsky
Publié dans: Database, 2022, ISSN 1758-0463
Éditeur: Oxford University Press
DOI: 10.1093/database/baac027