PIGS: automatic prediction of antibody structures. - Paolo Marcatili; Alessandra Rosi; Anna Tramontano (Bioinform., 2008)

FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. - Gabriele Ausiello; Pier Federico Gherardini; Paolo Marcatili; Anna Tramontano; Allegra Via; Manuela Helmer-Citterich (BMC Bioinform., 2008)

The MoVIN server for the analysis of protein interaction networks. - Paolo Marcatili; Giovanni Bussotti; Anna Tramontano (BMC Bioinform., 2008)

Structural landscape of immunoglobulin lambda light chains. - Anna Chailyan; Davide Cirillo; Paolo Marcatili; Anna Tramontano (BCB, 2010)

PICMI: mapping point mutations on genomes. - Loredana Le Pera; Paolo Marcatili; Anna Tramontano (Bioinform., 2010)

MAISTAS: a tool for automatic structural evaluation of alternative splicing products. - Matteo Floris; Domenico Raimondo; Guido Leoni; Massimiliano Orsini; Paolo Marcatili; Anna Tramontano (Bioinform., 2011)

A database of immunoglobulins with integrated tools: DIGIT. - Anna Chailyan; Anna Tramontano; Paolo Marcatili (Nucleic Acids Res., 2012)

Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server. - Pier Paolo Olimpieri; Anna Chailyan; Anna Tramontano; Paolo Marcatili (Bioinform., 2013)

Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies. - Mario Abdel Messih; Rosalba Lepore; Paolo Marcatili; Anna Tramontano (Bioinform., 2014)

Tabhu: tools for antibody humanization. - Pier Paolo Olimpieri; Paolo Marcatili; Anna Tramontano (Bioinform., 2015)

LYRA, a webserver for lymphocyte receptor structural modeling. - Michael Schantz Klausen; Mads Valdemar Anderson; Martin Closter Jespersen; Morten Nielsen 001; Paolo Marcatili (Nucleic Acids Res., 2015)

Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity. - Lorenzo Asti; Guido Uguzzoni; Paolo Marcatili; Andrea Pagnani (PLoS Comput. Biol., 2016)

3D Protein-Structure-Oriented Discovery of Clinical Relation Across Chronic Lymphocytic Leukemia Patients. - Konstantinos Mochament; Andreas Agathangelidis; Eleftheria Polychronidou; Christos Palaskas; Elias Kalamaras; Panagiotis Moschonas; Kostas Stamatopoulos; Anna Chailyan; Nanna Overby; Paolo Marcatili; Anastasia Hadzidimitriou; Dimitrios Tzovaras (IWBBIO (2), 2017)

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. - Martin Closter Jespersen; Bjoern Peters; Morten Nielsen 001; Paolo Marcatili (Nucleic Acids Res., 2017)

Automated shape-based clustering of 3D immunoglobulin protein structures in chronic lymphocytic leukemia. - Eleftheria Polychronidou; Ilias Kalamaras; Andreas Agathangelidis; Lesley Ann Sutton; Xiao-Jie Yan; Vasilis Bikos; Anna Vardi; Konstantinos Mochament; Nicholas Chiorazzi; Chrysoula Belessi; Richard Rosenquist; Paolo Ghia; et al. (BMC Bioinform., 2018)

Benchmark datasets of immune receptor-epitope structural complexes. - Swapnil Mahajan; Zhen Yan; Martin Closter Jespersen; Kamilla Kjærgaard Jensen; Paolo Marcatili; Morten Nielsen 001; Alessandro Sette; Bjoern Peters (BMC Bioinform., 2019)

IEDB-AR: immune epitope database - analysis resource in 2019. - Sandeep Kumar Dhanda; Swapnil Mahajan; Sinu Paul; Zhen Yan; Haeuk Kim; Martin Closter Jespersen; Vanessa Isabell Jurtz; Massimo Andreatta; Jason A. Greenbaum; Paolo Marcatili; Alessandro Sette; Morten Nielsen 001; et al. (Nucleic Acids Res., 2019)

proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking. - Francesco Ambrosetti; Tobias Hegelund Olsen; Pier Paolo Olimpieri; Brian Jiménez-García; Edoardo Milanetti; Paolo Marcatili; Alexandre M. J. J. Bonvin (Bioinform., 2020)

The ABCD database: a repository for chemically defined antibodies. - Wanessa C. Lima; Elisabeth Gasteiger; Paolo Marcatili; Paula Duek Roggli; Amos Bairoch; Pierre Cosson (Nucleic Acids Res., 2020)

NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning. - Magnus Haraldson Høie; Erik Nicolas Kiehl; Bent Petersen; Morten Nielsen 001; Ole Winther; Henrik Nielsen; Jeppe Hallgren; Paolo Marcatili (Nucleic Acids Res., 2022)