Functional Rotation of the Transporter AcrB: Insights into Drug Extrusion from Simulations. - Robert Schulz; Attilio Vittorio Vargiu; Francesca Collu; Ulrich Kleinekathöfer; Paolo Ruggerone (PLoS Comput. Biol., 2010)

Molecular motions in drug design: the coming age of the metadynamics method. - Xevi Biarnés; Salvatore Bongarzone; Attilio Vittorio Vargiu; Paolo Carloni; Paolo Ruggerone (J. Comput. Aided Mol. Des., 2011)

Extracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case. - Giuliano Malloci; Giovanni Serra; Andrea Bosin; Attilio Vittorio Vargiu (Comput., 2016)

Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape. - Andrea Basciu; Giuliano Malloci; Fabio Pietrucci; Alexandre M. J. J. Bonvin; Attilio Vittorio Vargiu (J. Chem. Inf. Model., 2019)

Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4. - Andrea Basciu; Panagiotis I. Koukos; Giuliano Malloci; Alexandre M. J. J. Bonvin; Attilio Vittorio Vargiu (J. Comput. Aided Mol. Des., 2020)

Machine Learning Integrating Protein Structure, Sequence, and Dynamics to Predict the Enzyme Activity of Bovine Enterokinase Variants. - Niccolo Alberto Elia Venanzi; Andrea Basciu; Attilio Vittorio Vargiu; Alexandros Kiparissides; Paul A. Dalby; Duygu Dikicioglu (J. Chem. Inf. Model., 2024)

Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins. - Andrea Basciu; Mohd Athar; Han Kurt; Christine Neville; Giuliano Malloci; Fabrizio C. Muredda; Andrea Bosin; Paolo Ruggerone; Alexandre M. J. J. Bonvin; Attilio Vittorio Vargiu (J. Chem. Inf. Model., 2025)