Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects. - José D. Faraldo-Gómez; Benoît Roux (J. Comput. Chem., 2007)

Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg2+ through the SOMA string method. - Davide Branduardi; Fabrizio Marinelli 002; José D. Faraldo-Gómez (J. Comput. Chem., 2016)

Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics. - Giacomo Fiorin; Fabrizio Marinelli 002; José D. Faraldo-Gómez (J. Comput. Chem., 2020)