Damiano Piovesan

Publication Activity (10 Years)

Years Active: 2011-2024
Publications (10 Years): 33

Top Topics

Intrinsically Disordered

Protein Structure

Molecular Dynamics

Top Venues

Nucleic Acids Res.

Database J. Biol. Databases Curation

Publications

Federica Quaglia, Anastasia Chasapi, Maria Victoria Nugnes, Maria Cristina Aspromonte, Emanuela Leonardi, Damiano Piovesan, Silvio C. E. Tosatto
Best practices for the manual curation of intrinsically disordered proteins in DisProt. Database J. Biol. Databases Curation 2024 (2024)
Damiano Piovesan, Davide Zago, Parnal Joshi, M. Clara De Paolis Kaluza, Alexander Miguel Monzon, Walter Reade, Iddo Friedberg, Predrag Radivojac, Silvio C. E. Tosatto
CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods. CoRR (2023)
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
MobiDB: 10 years of intrinsically disordered proteins. Nucleic Acids Res. 51 (D1) (2023)
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, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M. Krautheimer, Michael Bernhofer, Liam J. McGuffin, Isabelle Callebaut, Tristan Bitard Feildel, Jian Liu, Jianlin Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg Gsponer, Chol-Song Kim, Kun-Sop Han, Myong-Chol Ma, Lukasz A. Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md. Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu. Lobanov, Oxana V. Galzitskaya, Wim F. Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip K. Paliwal, Zsuzsanna Dosztányi, Gábor Erdös, Silvio C. E. Tosatto, Damiano Piovesan
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. Nucleic Acids Res. 51 (W1) (2023)
Alessio Del Conte, Alexander Miguel Monzon, Damiano Clementel, Giorgia F. Camagni, Giovanni Minervini, Silvio C. E. Tosatto, Damiano Piovesan
RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics. Bioinform. 39 (5) (2023)
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, Erzsébet Fichó, Maria Cristina Aspromonte, Claudio Bassot, Anastasia Chasapi, Norman E. Davey, Radoslav Davidovic, Laszlo Dobson, Arne Elofsson, Gábor Erdös, Pascale Gaudet, Michelle G. Giglio, Juliana Glavina, Javier Iserte, Valentín Iglesias, Zsófia L. Kálmán, Matteo Lambrughi, Emanuela Leonardi, Sonia Longhi, Sandra Macedo-Ribeiro, Emiliano Maiani, Julia Marchetti, Cristina Marino Buslje, Attila Meszaros, Alexander Miguel Monzon, Giovanni Minervini, Suvarna Nadendla, Juliet F. Nilsson, Marián Novotný, Christos A. Ouzounis, Nicolas Palopoli, Elena Papaleo, Pedro J. Barbosa Pereira, Gabriele Pozzati, Vasilis J. Promponas, Jordi Pujols, Alma Carolina Sanchez Rocha, Martin Salas, Luciana Rodriguez Sawicki, Éva Schád, Aditi Shenoy, Tamás Szaniszló, Konstantinos D. Tsirigos, Nevena Veljkovic, Gustavo D. Parisi, Salvador Ventura, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto, Damiano Piovesan
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. Nucleic Acids Res. 50 (D1) (2022)
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, Geoffrey J. Barton, David Bednar, Karel Berka, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Pawel Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar Sánchez Sorzano, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar
PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 50 (D1) (2022)
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 Res. 50 (W1) (2022)
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. Bioinform. 38 (4) (2022)
András Hatos, Alexander Miguel Monzon, Silvio C. E. Tosatto, Damiano Piovesan, Mónika Fuxreiter
FuzDB: a new phase in understanding fuzzy interactions. Nucleic Acids Res. 50 (D1) (2022)
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, Gustavo D. Parisi, Mónika Fuxreiter, Silvio C. E. Tosatto
MobiDB: intrinsically disordered proteins in 2021. Nucleic Acids Res. 49 (Database-Issue) (2021)
Marco Necci, Damiano Piovesan, Damiano Clementel, Zsuzsanna Dosztányi, Silvio C. E. Tosatto
MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins. Bioinform. 36 (22-23) (2021)
András Hatos, Federica Quaglia, Damiano Piovesan, Silvio C. E. Tosatto
APICURON: a database to credit and acknowledge the work of biocurators. Database J. Biol. Databases Curation 2021 (2021)
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, Maia Cabrera, Martin Gonzalez Buitron, Mariane Gonçalves Kulik, Sebastian Fernandez Alberti, María Silvina Fornasari, Gustavo D. 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 Res. 49 (Database-Issue) (2021)
Damiano Piovesan, András Hatos, Giovanni Minervini, Federica Quaglia, Alexander Miguel Monzon, Silvio C. E. Tosatto
Assessing predictors for new post translational modification sites: A case study on hydroxylation. PLoS Comput. Biol. 16 (6) (2020)
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. Bioinform. 36 (10) (2020)
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 Res. 48 (Webserver-Issue) (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, Radoslav Davidovic, A. Keith Dunker, Arne Elofsson, Julien Gobeill, Nicolás S. González Foutel, Govindarajan Sudha, Mainak Guharoy, Tamás Horváth, Valentin Iglesias, Andrey V. Kajava, Orsolya P. Kovács, John Lamb, Matteo Lambrughi, Tamas Lazar, Jeremy Y. Leclercq, Emanuela Leonardi, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Emiliano Maiani, José A. Manso, Cristina Marino Buslje, Elizabeth Martínez-Pérez, Bálint Mészáros, Ivan Micetic, Giovanni Minervini, Nikoletta Murvai, Marco Necci, Christos A. Ouzounis, Mátyás Pajkos, Lisanna Paladin, Rita Pancsa, Elena Papaleo, Gustavo D. Parisi, Emilie Pasche, Pedro J. Barbosa Pereira, Vasilis J. Promponas, Jordi Pujols, Federica Quaglia, Patrick Ruch, Marco Salvatore, Éva Schád, Beáta Szabó, Tamás Szaniszló, Stella Tamana, Ágnes Tantos, Nevena Veljkovic, Salvador Ventura, Wim F. Vranken, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto, Damiano Piovesan
DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res. 48 (Database-Issue) (2020)
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, Lisanna Paladin, Damiano Piovesan, Silvio C. E. Tosatto, Robert D. Finn
The Pfam protein families database in 2019. Nucleic Acids Res. 47 (Database-Issue) (2019)
Damiano Piovesan, Silvio C. E. Tosatto
INGA 2.0: improving protein function prediction for the dark proteome. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
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, Pietro Sormanni, Peter Tompa, Michele Vendruscolo, Wim F. Vranken, Silvio C. E. Tosatto
MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. Nucleic Acids Res. 46 (Database-Issue) (2018)
Marco Necci, Damiano Piovesan, Silvio C. E. Tosatto
Where differences resemble: sequence-feature analysis in curated databases of intrinsically disordered proteins. Database J. Biol. Databases Curation 2018 (2018)
Layla Hirsh, Lisanna Paladin, Damiano Piovesan, Silvio C. E. Tosatto
RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Damiano Piovesan, Silvio C. E. Tosatto
Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures. Bioinform. 34 (1) (2018)
Marco Necci, Damiano Piovesan, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto
A comprehensive assessment of long intrinsic protein disorder from the DisProt database. Bioinform. 34 (3) (2018)
Marco Necci, Damiano Piovesan, Diego Micheletti, Lisanna Paladin, Alessandro Cestaro, Silvio C. E. Tosatto
PhytoTypeDB: a database of plant protein inter-cultivar variability and function. Database J. Biol. Databases Curation 2018 (2018)
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, András Hatos, Andrey V. Kajava, Lajos Kalmár, Emanuela Leonardi, Tamas Lazar, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Attila Meszaros, Giovanni Minervini, Nikoletta Murvai, Jordi Pujols, Daniel B. Roche, Edoardo Salladini, Éva Schád, Antoine Schramm, Beáta Szabó, Ágnes Tantos, Fiorella Tonello, Konstantinos D. Tsirigos, Nevena Veljkovic, Salvador Ventura, Wim F. Vranken, Per Warholm, Vladimir N. Uversky, A. Keith Dunker, Sonia Longhi, Peter Tompa, Silvio C. E. Tosatto
DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res. 45 (Database-Issue) (2017)
Lisanna Paladin, Layla Hirsh, Damiano Piovesan, Miguel A. Andrade-Navarro, Andrey V. Kajava, Silvio C. E. Tosatto
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures. Nucleic Acids Res. 45 (Database-Issue) (2017)
Marco Necci, Damiano Piovesan, Zsuzsanna Dosztányi, Silvio C. E. Tosatto
MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins. Bioinform. 33 (9) (2017)
Damiano Piovesan, Ian Walsh, Giovanni Minervini, Silvio C. E. Tosatto
FELLS: fast estimator of latent local structure. Bioinform. 33 (12) (2017)
Lisanna Paladin, Damiano Piovesan, Silvio C. E. Tosatto
SODA: prediction of protein solubility from disorder and aggregation propensity. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L. Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Youngmi Park, Sebastien Pesseat, Damiano Piovesan, Simon C. Potter, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Ioannis Xenarios, Lai-Su L. Yeh, Siew-Yit Yong, Alex L. Mitchell
InterPro in 2017 - beyond protein family and domain annotations. Nucleic Acids Res. 45 (Database-Issue) (2017)
Damiano Piovesan, Giovanni Minervini, Silvio C. E. Tosatto
The RING 2.0 web server for high quality residue interaction networks. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Layla Hirsh, Damiano Piovesan, Manuel Giollo, Carlo Ferrari, Silvio C. E. Tosatto
The Victor C++ library for protein representation and advanced manipulation. Bioinform. 31 (7) (2015)
Damiano Piovesan, Manuel Giollo, Emanuela Leonardi, Carlo Ferrari, Silvio C. E. Tosatto
INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
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
RepeatsDB: a database of tandem repeat protein structures. Nucleic Acids Res. 42 (Database-Issue) (2014)
Giuseppe Profiti, Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
Protein Sequence Annotation by means of Community Detection. IWBBIO (2013)
Giuseppe Profiti, Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
Community Detection within Clusters Helps Large Scale Protein Annotation - Preliminary Results of Modularity Maximization for the BAR+ Database. BIOINFORMATICS (2013)
Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
Extended and Robust Protein Sequence Annotation over Conservative Nonhierarchical Clusters: The Case Study of the ABC Transporters. ACM J. Emerg. Technol. Comput. Syst. 9 (4) (2013)
Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Giuseppe Profiti, Andrea Zauli, Ivan Rossi, Rita Casadio
How to inherit statistically validated annotation within BAR+ protein clusters. BMC Bioinform. 14 (S-3) (2013)
Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Piero Fariselli, Luca Fontanesi, Rita Casadio
SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation. Database J. Biol. Databases Curation 2013 (2013)
Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio
The human "magnesome": detecting magnesium binding sites on human proteins. BMC Bioinform. 13 (S-14) (2012)
Castrense Savojardo, Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, Rita Casadio
Machine-Learning Methods to Predict Protein Interaction Sites in Folded Proteins. CIBB (2011)
Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Andrea Zauli, Ivan Rossi, Rita Casadio
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)