Repeat protein Function Refinement, Annotation and Classification of Topologies

Informacje na temat projektu

REFRACT

Identyfikator umowy o grant: 823886

DOI

10.3030/823886

Projekt został zamknięty

Data podpisania przez KE 26 Października 2018

Data rozpoczęcia 1 Stycznia 2019

Data zakończenia 30 Czerwca 2024

Finansowanie w ramach

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Koszt całkowity

€ 2 392 000,00

Wkład UE

€ 2 226 400,00

Koordynowany przez

UNIVERSITA DEGLI STUDI DI PADOVA
Italy

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Rezultaty

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)

Publikacje

Peer reviewed articles (41)

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

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

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

Autorzy: Del Conte A.; Monzon A. M.; Clementel D.; Camagni G. F.; Minervini G.; Tosatto S. C. E.; Piovesan D.
Opublikowane w: Bioinformatics, Numer 16, 2023, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btad260

Prokaryotic membrane coat - like proteins: An update

Autorzy: M. Leticia Ferrelli; Matías L. Pidre; Ruben García-Domínguez; Lucas N. Alberca; DMaría del Saz-Navarro; Carlos Santana-Molina; Damien P. Devos
Opublikowane w: Journal of Structural Biology, Numer 8, 2023, ISSN 1047-8477
Wydawca: 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

Autorzy: Martina Bevilacqua, Lisanna Paladin, Silvio C E Tosatto, Damiano Piovesan
Opublikowane w: Bioinformatics, 2021, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btab764

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

Autorzy: Matteo Delucchi, Elke Schaper, Oxana Sachenkova, Arne Elofsson and Maria Anisimova
Opublikowane w: Genes, 2020, ISSN 2073-4425
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes11040407

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

Autorzy: Pablo Mier, Carlos A Elena-Real, Juan Cortés, Pau Bernadó, Miguel A Andrade-Navarro
Opublikowane w: Bioinformatics, 2022, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btac610

The nucleotide landscape of polyXY regions

Autorzy: Pablo Mier, Miguel A. Andrade-Navarro
Opublikowane w: Computational and Structural Biotechnology Journal, Numer 21, 2024, Strona(/y) 5408-5412, ISSN 2001-0370
Wydawca: Elsevier
DOI: 10.1016/j.csbj.2023.10.054

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

Autorzy: Gustavo Parisi; Nicolas Palopoli; Silvio C. E. Tosatto; María Silvina Fornasari; Peter Tompa
Opublikowane w: Current Research in Structural Biology, Numer 8, 2021, ISSN 2665-928X
Wydawca: Elsevier
DOI: 10.1016/j.crstbi.2021.06.002

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

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

DOME: recommendations for supervised machine learning validation in biology

Autorzy: 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
Opublikowane w: Nature Methods, 2021, ISSN 1548-7091
Wydawca: 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

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

Census of exposed aggregation-prone regions in proteomes

Autorzy: Théo Falgarone, Etienne Villain, Francois Richard, Zarifa Osmanli, Andrey V Kajava
Opublikowane w: Briefings in Bioinformatics, 2023, ISSN 1467-5463
Wydawca: Oxford University Press
DOI: 10.1093/bib/bbad183

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

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

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

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

Daisy: An integrated repeat protein curation service

Autorzy: Manuel, Bezerra-Brandao; Ronaldo Romario, Tunque Cahui; Layla, Hirsh
Opublikowane w: Journal of Structural Biology, Numer 6, 2023, ISSN 1047-8477
Wydawca: Academic Press
DOI: 10.1016/j.jsb.2023.108033

Structured Tandem Repeats in Protein Interactions

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

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

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

Structure-function relationships in protein homorepeats

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

Protein repeats evolve and emerge in giant viruses

Autorzy: Erdozain Bagolin, Sofía Agostina; Barrionuevo, Emilia Mercedes; Ripoll, Lucas; Mier, Pablo; Andrade Navarro, Miguel A.
Opublikowane w: Journal of Structural Biology, Numer 11, 2023, ISSN 1047-8477
Wydawca: Academic Press
DOI: 10.1016/j.jsb.2023.107962

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

Autorzy: Vladimir Perovic; Jeremy Y Leclercq; Neven Sumonja; Francois Richard; Francois Richard; Nevena Veljkovic; Andrey V. Kajava
Opublikowane w: Bioinformatics, Numer 8, 2020, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btaa121

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

Autorzy: Escobedo N, Monzon AM, Fornasari MS, Palopoli N, Parisi G
Opublikowane w: Current Protocols, 2023, ISSN 2691-1299
Wydawca: John Wiley & Sons
DOI: 10.1002/cpz1.764

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

Autorzy: 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
Opublikowane w: Nucleic Acids Research, Numer 4, 2021, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkaa1097

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

Autorzy: Manasra S, Kajava AV
Opublikowane w: Journal of Structural Biology, 2023, ISSN 1047-8477
Wydawca: Academic Press
DOI: 10.1016/j.jsb.2023.108014

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

Autorzy: Del Conte A.; Mehdiabadi M.; Bouhraoua A.; Monzon A. M.; Tosatto S. C. E.; Piovesan D.
Opublikowane w: Proteins: Structure, Function and Bioinformatics, Numer 15, 2023, ISSN 0887-3585
Wydawca: Wiley-Liss Inc
DOI: 10.1002/prot.26582

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

Autorzy: Claudio Bassot, Arne Elofsson
Opublikowane w: PLOS Computational Biology, 2021, ISSN 1553-734X
Wydawca: Public Library of Science
DOI: 10.1371/journal.pcbi.1008798

Expanding the repertoire of human tandem repeat RNA-binding proteins

Autorzy: Agustín Ormazábal; Matías Sebastián Carletti; Tadeo Enrique Saldaño; Martín Gonzalez-Buitron; Julia Marchetti; Nicolas Palopoli; Alex Bateman
Opublikowane w: PLoS ONE, Numer 11, 2023, ISSN 1932-6203
Wydawca: 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

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

Short tandem repeat mutations regulate gene expression in colorectal cancer

Autorzy: Max A. Verbiest; Oxana Lundström; Feifei Xia; Michael Baudis; Tugce Bilgin Sonay; Maria Anisimova
Opublikowane w: Scientific Reports, Numer 18, 2024, ISSN 2045-2322
Wydawca: 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

Autorzy: Max A. Verbiest, Matteo Delucchi, Tugce Bilgin Sonay and Maria Anisimova
Opublikowane w: Frontiers in Bioinformatics, 2021, ISSN 2673-7647
Wydawca: Frontiers Media
DOI: 10.3389/fbinf.2021.685844

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

Autorzy: András Hatos, Federica Quaglia, Damiano Piovesan, Silvio C E Tosatto
Opublikowane w: Database, 2021, ISSN 1758-0463
Wydawca: Oxford University Press
DOI: 10.1093/database/baab019

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

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

The features of polyglutamine regions depend on their evolutionary stability

Autorzy: Pablo Mier, Miguel A. Andrade-Navarro
Opublikowane w: BMC Ecology and Evolution, 2020, ISSN 2730-7182
Wydawca: 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

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

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

Autorzy: Mohamed Kamel, Kristina Kastano, Pablo Mier, Miguel A. Andrade
Opublikowane w: Journal of Molecular Biology, 2021, ISSN 0022-2836
Wydawca: Academic Press
DOI: 10.1016/j.jmb.2021.166895

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

Autorzy: 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
Opublikowane w: Nucleic Acids Research, Numer 16, 2024, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkad947

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

Autorzy: Matteo Delucchi; Paulina Näf; Spencer Bliven; Maria Anisimova
Opublikowane w: Frontiers in Bioinformatics, Numer 5, 2021, ISSN 2673-7647
Wydawca: Frontiers Media
DOI: 10.21256/zhaw-22764

Pfam: The protein families database in 2021.

Autorzy: 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
Opublikowane w: Nucleic Acids Research, Numer 5, 2020, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkaa913

A STRP-ed definition of Structured Tandem Repeats in Proteins

Autorzy: 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
Opublikowane w: Journal of Structural Biology, Numer 5, 2023, ISSN 1047-8477
Wydawca: Academic Press
DOI: 10.1016/j.jsb.2023.108023

DisProt in 2024: improving function annotation of intrinsically disordered proteins

Autorzy: 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;
Opublikowane w: Nucleic Acids Research, Numer 18, 2024, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkad928

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

Autorzy: 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
Opublikowane w: Nucleic Acids Research, Numer 7, 2020, ISSN 0305-1048
Wydawca: 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

Autorzy: Max Verbiest; Mikhail Maksimov; Ye Jin; Maria Anisimova; Melissa Gymrek; Tugce Bilgin Sonay
Opublikowane w: Journal of Evolutionary Biology, Numer 18, 2023, ISSN 1010-061X
Wydawca: 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

Autorzy: Federica Quaglia
Opublikowane w: Abstract booklet of the 14th Annual Biocuration Conference (virtual), including invited speakers talks and poster session presentations, 2021
Wydawca: 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

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

Conference proceedings (1)

Conference report: Biocuration 2021 Virtual Conference

Autorzy: Federica Quaglia, Rama Balakrishnan, Susan M Bello, Nicole Vasilevsky
Opublikowane w: Database, 2022, ISSN 1758-0463
Wydawca: Oxford University Press
DOI: 10.1093/database/baac027