VEGA - An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming. - Alessandro Pedretti; Luigi Villa; Giulio Vistoli (J. Comput. Aided Mol. Des., 2004)

Homology modeling and metabolism prediction of human carboxylesterase-2 using docking analyses by GriDock: a parallelized tool based on AutoDock 4.0. - Giulio Vistoli; Alessandro Pedretti; Angelica Mazzolari; Bernard Testa (J. Comput. Aided Mol. Des., 2010)

SPILLO-PBSS: Detecting hidden binding sites within protein 3D-structures through a flexible structure-based approach. - Alessandro Di Domizio; Alessandro Vitriolo; Giulio Vistoli; Alessandro Pedretti (J. Comput. Chem., 2014)

A computational model to predict the immune system activation by citrus-derived vaccine adjuvants. - Francesco Pappalardo 001; Epifanio Fichera; Nicoletta Paparone; Alessandro Lombardo; Marzio Pennisi; Giulia Russo; Marco Leotta; Alessandro Pedretti; Francesco De Fiore; Santo Motta (Bioinform., 2016)

Binding Space Concept: A New Approach To Enhance the Reliability of Docking Scores and Its Application to Predicting Butyrylcholinesterase Hydrolytic Activity. - Giulio Vistoli; Angelica Mazzolari; Bernard Testa; Alessandro Pedretti (J. Chem. Inf. Model., 2017)

WarpEngine, a Flexible Platform for Distributed Computing Implemented in the VEGA Program and Specially Targeted for Virtual Screening Studies. - Alessandro Pedretti; Angelica Mazzolari; Giulio Vistoli (J. Chem. Inf. Model., 2018)

FAME 3: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes. - Martin Sícho; Conrad Stork; Angelica Mazzolari; Christina de Bruyn Kops; Alessandro Pedretti; Bernard Testa; Giulio Vistoli; Daniel Svozil; Johannes Kirchmair (J. Chem. Inf. Model., 2019)

The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects. - Alessandro Pedretti; Angelica Mazzolari; Silvia Gervasoni; Laura Fumagalli; Giulio Vistoli (Bioinform., 2021)

GENEOnet: A new machine learning paradigm based on Group Equivariant Non-Expansive Operators. An application to protein pocket detection. - Giovanni Bocchi; Patrizio Frosini; Alessandra Micheletti; Alessandro Pedretti; Carmen Gratteri; Filippo Lunghini; Andrea Rosario Beccari; Carmine Talarico (CoRR, 2022)

SiteMap pockets for the PDBbind dataset. - Gianluca Palermo; Giovanni Bocchi; Carmine Talarico; Davide Gadioli; Alessandro Pedretti (Zenodo, 2023)

MUSA: A Platform for Data-Intensive Services in Edge-Cloud Continuum. - Marco Anisetti; Claudio A. Ardagna; Massimo Banzi; Filippo Berto; Ruslan Bondaruc; Ernesto Damiani; Alessandro Pedretti; Arianna Pisati; Antonio Retico (AINA (5), 2024)

A geometric XAI approach to protein pocket detection. - Giovanni Bocchi; Patrizio Frosini; Alessandra Micheletti; Alessandro Pedretti; Gianluca Palermo; Davide Gadioli; Carmen Gratteri; Filippo Lunghini; Andrea Rosario Beccari; Anna Fava; Carmine Talarico (xAI (Late-breaking Work, Demos, Doctoral Consortium), 2024)

Active Learning Approach for Guiding Site-of-Metabolism Measurement and Annotation. - Ya Chen 002; Thomas Seidel; Roxane Axel Jacob; Steffen Hirte; Angelica Mazzolari; Alessandro Pedretti; Giulio Vistoli; Thierry Langer; Filip Miljkovic; Johannes Kirchmair (J. Chem. Inf. Model., 2024)

"DompeKeys": a set of novel substructure-based descriptors for efficient chemical space mapping, development and structural interpretation of machine learning models, and indexing of large databases. - Candida Manelfi; Valerio Tazzari; Filippo Lunghini; Carmen Cerchia; Anna Fava; Alessandro Pedretti; Pieter F. W. Stouten; Giulio Vistoli; Andrea Rosario Beccari (J. Cheminformatics, 2024)

GENEOnet: Statistical analysis supporting explainability and trustworthiness. - Giovanni Bocchi; Patrizio Frosini; Alessandra Micheletti; Alessandro Pedretti; Carmen Gratteri; Filippo Lunghini; Andrea Rosario Beccari; Carmine Talarico (CoRR, 2025)