ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level. - Simone Marsili; Giorgio Federico Signorini; Riccardo Chelli; Massimo Marchi; Piero Procacci (J. Comput. Chem., 2010)

Insights into the Conformational Switching Mechanism of the Human Vascular Endothelial Growth Factor Receptor Type 2 Kinase Domain. - Matteo Chioccioli; Simone Marsili; Claudia Bonaccini; Piero Procacci; Paola Gratteri (J. Chem. Inf. Model., 2012)

Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones. - Duccio Malinverni; Simone Marsili; Alessandro Barducci; Paolo De Los Rios (PLoS Comput. Biol., 2015)

Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy. - Sudarshan Behera; David F. Hahn; Carter J. Wilson; Simone Marsili; Gary Tresadern; Vytautas Gapsys; Bert L. de Groot (J. Chem. Inf. Model., 2025)