Wordom: a program for efficient analysis of molecular dynamics simulations. - Michele Seeber; Marco Cecchini; Francesco Rao; Giovanni Settanni; Amedeo Caflisch (Bioinform., 2007)

Protein inherent structures by different minimization strategies. - Francesco Rao (J. Comput. Chem., 2011)

Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. - Michele Seeber; Angelo Felline; Francesco Raimondi 001; Stefanie Muff; Ran Friedman; Francesco Rao; Amedeo Caflisch; Francesca Fanelli (J. Comput. Chem., 2011)

Thermodynamics and kinetics of large-time-step molecular dynamics. - Francesco Rao; Martin Spichty (J. Comput. Chem., 2012)

Beyond the Binding Site: The Role of the β2 - β3 Loop and Extra-Domain Structures in PDZ Domains. - Stefano Mostarda; David Gfeller; Francesco Rao (PLoS Comput. Biol., 2012)