MonteGrappa: An iterative Monte Carlo program to optimize biomolecular potentials in simplified models. - Guido Tiana; Fulgencia Villa; Y. Zhan; Riccardo Capelli; Cristina Paissoni; Pietro Sormanni; Edith Heard; Luca Giorgetti; R. Meloni (Comput. Phys. Commun., 2015)

SAGE: A Fast Computational Tool for Linear Epitope Grafting onto a Foreign Protein Scaffold. - Riccardo Capelli; Filippo Marchetti; Guido Tiana; Giorgio Colombo 001 (J. Chem. Inf. Model., 2017)

Predictions of the Poses and Affinity of a Ligand over the Entire Surface of a NEET Protein: The Case of Human MitoNEET. - Ke Zuo; Riccardo Capelli; Giulia Rossetti; Rachel Nechushtai; Paolo Carloni (J. Chem. Inf. Model., 2023)

Machine Learning-Based Modeling of Olfactory Receptors in Their Inactive State: Human OR51E2 as a Case Study. - Mercedes Alfonso-Prieto; Riccardo Capelli (J. Chem. Inf. Model., 2023)

Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG. - Charly Empereur-mot; Kasper B. Pedersen; Riccardo Capelli; Martina Crippa; Cristina Caruso; Mattia Perrone; Paulo C. T. Souza; Siewert J. Marrink; Giovanni M. Pavan (J. Chem. Inf. Model., 2023)

Calcium-Driven In Silico Inactivation of a Human Olfactory Receptor. - Lorenza Pirona; Federico Ballabio; Mercedes Alfonso-Prieto; Riccardo Capelli (J. Chem. Inf. Model., 2024)

Role of Residues Undergoing Hereditary Spastic Paraplegias Mutations: Insights from Simulating the Spiral to Ring Transition in Katanin. - Maria S. Kelly; Riccardo Capelli; Ruxandra I. Dima; Paolo Carloni (J. Chem. Inf. Model., 2025)

Estimation of Ligand Binding Free Energy Using Multi-eGO. - Bruno Stegani; Emanuele Scalone; Fran Bacic Toplek; Thomas Löhr; Stefano Gianni; Michele Vendruscolo; Riccardo Capelli; Carlo Camilloni (J. Chem. Inf. Model., 2025)