Claudia Andreini - researchr alias

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Viewing Publication 1 - 15 from 15

2023

Hunting down zinc(II)-binding sites in proteins with distance matricesVincenzo Laveglia, Milana Bazayeva, Claudia Andreini, Antonio Rosato. bioinformatics, 39(10), October 2023. [doi]

2022

Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural NetworkVincenzo Laveglia, Andrea Giachetti 0002, Davide Sala, Claudia Andreini, Antonio Rosato. jcisd, 62(12):2951-2960, 2022. [doi]

PDBe-KB: collaboratively defining the biological context of structural dataMihaly 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 0001, 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. nar, 50(D1):534-542, 2022. [doi]

2019

Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein LigandsMarina Macchiagodena, Marco Pagliai, Claudia Andreini, Antonio Rosato, Piero Procacci. jcisd, 59(9):3803-3816, 2019. [doi]

2018

MetalPDB in 2018: a database of metal sites in biological macromolecular structuresValeria Putignano, Antonio Rosato, Lucia Banci, Claudia Andreini. nar, 46(Database-Issue), 2018. [doi]

2016

MetalPredator: a web server to predict iron-sulfur cluster binding proteomesYana Valasatava, Antonio Rosato, Lucia Banci, Claudia Andreini. bioinformatics, 32(18):2850-2852, 2016. [doi]

2013

2: A Tool for the Structural Alignment of Minimal Functional Sites in Metal-Binding Proteins and Nucleic AcidsClaudia Andreini, Gabriele Cavallaro, Antonio Rosato, Yana Valasatava. jcisd, 53(11):3064-3075, 2013. [doi]

MetalPDB: a database of metal sites in biological macromolecular structuresClaudia Andreini, Gabriele Cavallaro, Serena Lorenzini, Antonio Rosato. nar, 41(Database-Issue):312-319, 2013. [doi]

2012

FindGeo: a tool for determining metal coordination geometryClaudia Andreini, Gabriele Cavallaro, Serena Lorenzini. bioinformatics, 28(12):1658-1660, 2012. [doi]

MACiE: exploring the diversity of biochemical reactionsGemma L. Holliday, Claudia Andreini, Julia D. Fischer, Syed Asad Rahman, Daniel E. Almonacid, Sophie T. Williams, William R. Pearson. nar, 40(Database-Issue):783-789, 2012. [doi]

2011

A Simple Protocol for the Comparative Analysis of the Structure and Occurrence of Biochemical Pathways Across SuperkingdomsClaudia Andreini, Ivano Bertini, Gabriele Cavallaro, Leonardo Decaria, Antonio Rosato. jcisd, 51(3):730-738, 2011. [doi]

2009

Metal-MACiE: a database of metals involved in biological catalysisClaudia Andreini, Ivano Bertini, Gabriele Cavallaro, Gemma L. Holliday, Janet M. Thornton. bioinformatics, 25(16):2088-2089, 2009. [doi]

2007

Predicting zinc binding at the proteome levelAndrea Passerini, Claudia Andreini, Sauro Menchetti, Antonio Rosato, Paolo Frasconi. bmcbi, 8, 2007. [doi]

2006

Improving Prediction of Zinc Binding Sites by Modeling the Linkage Between Residues Close in SequenceSauro Menchetti, Andrea Passerini, Paolo Frasconi, Claudia Andreini, Antonio Rosato. recomb 2006: 309-320 [doi]

2004

A hint to search for metalloproteins in gene banksClaudia Andreini, Ivano Bertini, Antonio Rosato. bioinformatics, 20(9):1373-1380, 2004. [doi]

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