Machine-Learning Methods to Predict Protein Interaction Sites in Folded Proteins. - Castrense Savojardo; Piero Fariselli; Damiano Piovesan; Pier Luigi Martelli; Rita Casadio (CIBB, 2011)

BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences. - Damiano Piovesan; Pier Luigi Martelli; Piero Fariselli; Andrea Zauli; Ivan Rossi; Rita Casadio (Nucleic Acids Res., 2011)

The human "magnesome": detecting magnesium binding sites on human proteins. - Damiano Piovesan; Giuseppe Profiti; Pier Luigi Martelli; Rita Casadio (BMC Bioinform., 2012)

Community Detection within Clusters Helps Large Scale Protein Annotation - Preliminary Results of Modularity Maximization for the BAR+ Database. - Giuseppe Profiti; Damiano Piovesan; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (BIOINFORMATICS, 2013)

Protein Sequence Annotation by means of Community Detection. - Giuseppe Profiti; Damiano Piovesan; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (IWBBIO, 2013)

SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation. - Damiano Piovesan; Giuseppe Profiti; Pier Luigi Martelli; Piero Fariselli; Luca Fontanesi; Rita Casadio (Database J. Biol. Databases Curation, 2013)

How to inherit statistically validated annotation within BAR+ protein clusters. - Damiano Piovesan; Pier Luigi Martelli; Piero Fariselli; Giuseppe Profiti; Andrea Zauli; Ivan Rossi; Rita Casadio (BMC Bioinform., 2013)

Extended and Robust Protein Sequence Annotation over Conservative Nonhierarchical Clusters: The Case Study of the ABC Transporters. - Damiano Piovesan; Giuseppe Profiti; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (ACM J. Emerg. Technol. Comput. Syst., 2013)

RepeatsDB: a database of tandem repeat protein structures. - Tomás Di Domenico; Emilio Potenza; Ian Walsh; R. Gonzalo Parra; Manuel Giollo; Giovanni Minervini; Damiano Piovesan; Awais Ihsan; Carlo Ferrari; Andrey V. Kajava; Silvio C. E. Tosatto (Nucleic Acids Res., 2014)

The Victor C++ library for protein representation and advanced manipulation. - Layla Hirsh; Damiano Piovesan; Manuel Giollo; Carlo Ferrari; Silvio C. E. Tosatto (Bioinform., 2015)

INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity. - Damiano Piovesan; Manuel Giollo; Emanuela Leonardi; Carlo Ferrari; Silvio C. E. Tosatto (Nucleic Acids Res., 2015)

The RING 2.0 web server for high quality residue interaction networks. - Damiano Piovesan; Giovanni Minervini; Silvio C. E. Tosatto (Nucleic Acids Res., 2016)

MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins. - Marco Necci; Damiano Piovesan; Zsuzsanna Dosztányi; Silvio C. E. Tosatto (Bioinform., 2017)

FELLS: fast estimator of latent local structure. - Damiano Piovesan; Ian Walsh; Giovanni Minervini; Silvio C. E. Tosatto (Bioinform., 2017)

InterPro in 2017 - beyond protein family and domain annotations. - Robert D. Finn; Teresa K. Attwood; Patricia C. Babbitt; Alex Bateman; Peer Bork; Alan J. Bridge; Hsin-Yu Chang; Zsuzsanna Dosztányi; Sara El-Gebali; Matthew Fraser; Julian Gough; David Haft; et al. (Nucleic Acids Res., 2017)

RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures. - Lisanna Paladin; Layla Hirsh; Damiano Piovesan; Miguel A. Andrade-Navarro; Andrey V. Kajava; Silvio C. E. Tosatto (Nucleic Acids Res., 2017)

SODA: prediction of protein solubility from disorder and aggregation propensity. - Lisanna Paladin; Damiano Piovesan; Silvio C. E. Tosatto (Nucleic Acids Res., 2017)

DisProt 7.0: a major update of the database of disordered proteins. - Damiano Piovesan; Francesco Tabaro; Ivan Micetic; Marco Necci; Federica Quaglia; Christopher J. Oldfield; Maria Cristina Aspromonte; Norman E. Davey; Radoslav Davidovic; Zsuzsanna Dosztányi; Arne Elofsson; Alessandra Gasparini; et al. (Nucleic Acids Res., 2017)

PhytoTypeDB: a database of plant protein inter-cultivar variability and function. - Marco Necci; Damiano Piovesan; Diego Micheletti; Lisanna Paladin; Alessandro Cestaro; Silvio C. E. Tosatto (Database J. Biol. Databases Curation, 2018)

Where differences resemble: sequence-feature analysis in curated databases of intrinsically disordered proteins. - Marco Necci; Damiano Piovesan; Silvio C. E. Tosatto (Database J. Biol. Databases Curation, 2018)

A comprehensive assessment of long intrinsic protein disorder from the DisProt database. - Marco Necci; Damiano Piovesan; Zsuzsanna Dosztányi; Peter Tompa; Silvio C. E. Tosatto (Bioinform., 2018)

Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures. - Damiano Piovesan; Silvio C. E. Tosatto (Bioinform., 2018)

RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins. - Layla Hirsh; Lisanna Paladin; Damiano Piovesan; Silvio C. E. Tosatto (Nucleic Acids Res., 2018)

MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. - Damiano Piovesan; Francesco Tabaro; Lisanna Paladin; Marco Necci; Ivan Micetic; Carlo Camilloni; Norman E. Davey; Zsuzsanna Dosztányi; Bálint Mészáros; Alexander Miguel Monzon; Gustavo D. Parisi; Éva Schád; et al. (Nucleic Acids Res., 2018)

The Pfam protein families database in 2019. - Sara El-Gebali; Jaina Mistry; Alex Bateman; Sean R. Eddy; Aurelien Luciani; Simon C. Potter; Matloob Qureshi; Lorna J. Richardson; Gustavo A. Salazar; Alfredo Smart; Erik L. L. Sonnhammer; Layla Hirsh; et al. (Nucleic Acids Res., 2019)

INGA 2.0: improving protein function prediction for the dark proteome. - Damiano Piovesan; Silvio C. E. Tosatto (Nucleic Acids Res., 2019)

The Feature-Viewer: a visualization tool for positional annotations on a sequence. - Lisanna Paladin; Mathieu Schaeffer; Pascale Gaudet; Monique Zahn-Zabal; Pierre-André Michel; Damiano Piovesan; Silvio C. E. Tosatto; Amos Bairoch (Bioinform., 2020)

DisProt: intrinsic protein disorder annotation in 2020. - András Hatos; Borbála Hajdu-Soltész; Alexander Miguel Monzon; Nicolas Palopoli; Lucía Álvarez; Burcu Aykaç Fas; Claudio Bassot; Guillermo I. Benítez; Martina Bevilacqua; Anastasia Chasapi; Lucía B. Chemes; Norman E. Davey; et al. (Nucleic Acids Res., 2020)

PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins. - 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; et al. (Nucleic Acids Res., 2020)

Assessing predictors for new post translational modification sites: A case study on hydroxylation. - Damiano Piovesan; András Hatos; Giovanni Minervini; Federica Quaglia; Alexander Miguel Monzon; Silvio C. E. Tosatto (PLoS Comput. Biol., 2020)

APICURON: a database to credit and acknowledge the work of biocurators. - András Hatos; Federica Quaglia; Damiano Piovesan; Silvio C. E. Tosatto (Database J. Biol. Databases Curation, 2021)

MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins. - Marco Necci; Damiano Piovesan; Damiano Clementel; Zsuzsanna Dosztányi; Silvio C. E. Tosatto (Bioinform., 2021)

RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures. - Lisanna Paladin; Martina Bevilacqua; Sara Errigo; Damiano Piovesan; Ivan Micetic; Marco Necci; Alexander Miguel Monzon; Maria Laura Fabre; José Luis López; Juliet F. Nilsson; Javier Ríos; Pablo Lorenzano Menna; et al. (Nucleic Acids Res., 2021)

MobiDB: intrinsically disordered proteins in 2021. - Damiano Piovesan; Marco Necci; Nahuel Escobedo; Alexander Miguel Monzon; András Hatos; Ivan Micetic; Federica Quaglia; Lisanna Paladin; Pathmanaban Ramasamy; Zsuzsanna Dosztányi; Wim F. Vranken; Norman E. Davey; et al. (Nucleic Acids Res., 2021)

ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications. - Martina Bevilacqua; Lisanna Paladin; Silvio C. E. Tosatto; Damiano Piovesan (Bioinform., 2022)

RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles. - Damiano Clementel; Alessio Del Conte; Alexander Miguel Monzon; Giorgia F. Camagni; Giovanni Minervini; Damiano Piovesan; Silvio C. E. Tosatto (Nucleic Acids Res., 2022)

FuzDB: a new phase in understanding fuzzy interactions. - András Hatos; Alexander Miguel Monzon; Silvio C. E. Tosatto; Damiano Piovesan; Mónika Fuxreiter (Nucleic Acids Res., 2022)

DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. - Federica Quaglia; Bálint Mészáros; Edoardo Salladini; András Hatos; Rita Pancsa; Lucía B. Chemes; Mátyás Pajkos; Tamas Lazar; Samuel Peña-Díaz; Jaime Santos; Veronika Ács; Nazanin Farahi; et al. (Nucleic Acids Res., 2022)

PDBe-KB: collaboratively defining the biological context of structural data. - Mihaly Varadi; Stephen Anyango; David R. Armstrong; John M. Berrisford; Preeti Choudhary; Mandar S. Deshpande; Nurul Nadzirin; Sreenath Nair; Lukás Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; et al. (Nucleic Acids Res., 2022)

CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods. - Damiano Piovesan; Davide Zago; Parnal Joshi; M. Clara De Paolis Kaluza; Alexander Miguel Monzon; Walter Reade; Iddo Friedberg; Predrag Radivojac; Silvio C. E. Tosatto (CoRR, 2023)

MobiDB: 10 years of intrinsically disordered proteins. - Damiano Piovesan; Alessio Del Conte; Damiano Clementel; Alexander Miguel Monzon; Martina Bevilacqua; Maria Cristina Aspromonte; Javier Iserte; Fernando E. Orti; Cristina Marino Buslje; Silvio C. E. Tosatto (Nucleic Acids Res., 2023)

RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics. - Alessio Del Conte; Alexander Miguel Monzon; Damiano Clementel; Giorgia F. Camagni; Giovanni Minervini; Silvio C. E. Tosatto; Damiano Piovesan (Bioinform., 2023)

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. - Alessio Del Conte; Adel Bouhraoua; Mahta Mehdiabadi; Damiano Clementel; Alexander Miguel Monzon; Alex S. Holehouse; Daniel A. Griffith; Ryan J. Emenecker; Ashwini Patil; Ronesh Sharma; Tatsuhiko Tsunoda; Alok Sharma; et al. (Nucleic Acids Res., 2023)

Best practices for the manual curation of intrinsically disordered proteins in DisProt. - Federica Quaglia; Anastasia Chasapi; Maria Victoria Nugnes; Maria Cristina Aspromonte; Emanuela Leonardi; Damiano Piovesan; Silvio C. E. Tosatto (Database J. Biol. Databases Curation, 2024)