DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis. - Simone Aureli; Daniele Di Marino; Stefano Raniolo; Vittorio Limongelli (Bioinform., 2019)

Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein-Ligand Binding Poses. - Dominykas Lukauskis; Marley L. Samways; Simone Aureli; Benjamin P. Cossins; Richard D. Taylor; Francesco Luigi Gervasio (J. Chem. Inf. Model., 2022)

Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study. - Simone Aureli; Francesco Bellina; Valerio Rizzi; Francesco Luigi Gervasio (J. Chem. Inf. Model., 2024)

Learning committor-consistent collective variables. - Thorben Fröhlking; Simone Aureli; Francesco Luigi Gervasio (Nat. Comput. Sci., 2025)