PLUMED: A portable plugin for free-energy calculations with molecular dynamics. - Massimiliano Bonomi; Davide Branduardi; Giovanni Bussi; Carlo Camilloni; Davide Provasi; Paolo Raiteri; Davide Donadio; Fabrizio Marinelli 002; Fabio Pietrucci; Ricardo A. Broglia; Michele Parrinello (Comput. Phys. Commun., 2009)

A chirality-based metrics for free-energy calculations in biomolecular systems. - Adriana Pietropaolo; Davide Branduardi; Massimiliano Bonomi; Michele Parrinello (J. Comput. Chem., 2011)

PLUMED 2: New feathers for an old bird. - Gareth A. Tribello; Massimiliano Bonomi; Davide Branduardi; Carlo Camilloni; Giovanni Bussi (Comput. Phys. Commun., 2014)

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)