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2020 – today
- 2024
[j40]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)- 2023
- [j39]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) - [j38]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): 438-444 (2023) - [j37]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): 62-69 (2023) - [i1]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 abs/2310.06881 (2023) - 2022
- [j36]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): 1129-1130 (2022) - [j35]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): 480-487 (2022) - [j34]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): 509-517 (2022) - [j33]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): 534-542 (2022) - [j32]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): 651-656 (2022) - 2021
- [j31]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) - [j30]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): 5533-5534 (2021) - [j29]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): D361-D367 (2021) - [j28]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): D452-D457 (2021) - 2020
- [j27]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): 3244-3245 (2020) - [j26]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): D269-D276 (2020) - [j25]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): W77-W84 (2020) - [j24]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)
2010 – 2019
- 2019
- [j23]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): D427-D432 (2019) - [j22]Damiano Piovesan, Silvio C. E. Tosatto:
INGA 2.0: improving protein function prediction for the dark proteome. Nucleic Acids Res. 47(Webserver-Issue): W373-W378 (2019) - 2018
- [j21]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: bay125 (2018) - [j20]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: bay127 (2018) - [j19]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): 122-123 (2018) - [j18]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): 445-452 (2018) - [j17]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): D471-D476 (2018) - [j16]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): W402-W407 (2018) - 2017
- [j15]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): 1402-1404 (2017) - [j14]Damiano Piovesan, Ian Walsh, Giovanni Minervini, Silvio C. E. Tosatto:
FELLS: fast estimator of latent local structure. Bioinform. 33(12): 1889-1891 (2017) - [j13]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, 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, Young Mi 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): D190-D199 (2017) - [j12]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): D219-D227 (2017) - [j11]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): D308-D312 (2017) - [j10]Lisanna Paladin, Damiano Piovesan, Silvio C. E. Tosatto:
SODA: prediction of protein solubility from disorder and aggregation propensity. Nucleic Acids Res. 45(Webserver-Issue): W236-W240 (2017) - 2016
- [j9]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): W367-W374 (2016) - 2015
- [j8]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): 1138-1140 (2015) - [j7]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): W134-W140 (2015) - 2014
- [j6]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): 352-357 (2014) - 2013
- [j5]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) - [j4]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): S4 (2013) - [j3]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): 27:1-27:8 (2013) - [c3]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: 328-332 - [c2]Giuseppe Profiti, Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
Protein Sequence Annotation by means of Community Detection. IWBBIO 2013: 753-755 - 2012
- [j2]Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio:
The human "magnesome": detecting magnesium binding sites on human proteins. BMC Bioinform. 13(S-14): S10 (2012) - 2011
- [j1]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): 197-202 (2011) - [c1]Castrense Savojardo, Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, Rita Casadio:
Machine-Learning Methods to Predict Protein Interaction Sites in Folded Proteins. CIBB 2011: 127-135
Coauthor Index
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