Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands. - Marina Macchiagodena; Marco Pagliai; Claudia Andreini; Antonio Rosato; Piero Procacci (J. Chem. Inf. Model., 2019)

On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge. - Piero Procacci; Marina Macchiagodena (J. Comput. Aided Mol. Des., 2021)

Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS. - Marina Macchiagodena; Maurice Karrenbrock; Marco Pagliai; Piero Procacci (J. Chem. Inf. Model., 2021)

NE-RDFE: A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes. - Marina Macchiagodena; Marco Pagliai; Piero Procacci (J. Comput. Chem., 2023)