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)

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics. - Massimiliano Bonomi; Alessandro Barducci; Michele Parrinello (J. Comput. Chem., 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)

The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery. - Lili X. Peng; Monica T. Hsu; Massimiliano Bonomi; David A. Agard; Matthew P. Jacobson (PLoS Comput. Biol., 2014)

Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening. - Claire Colas; Christof Grewer; Nicholas James Otte; Armanda Gameiro; Thomas Albers; Kurnvir Singh; Helen Shere; Massimiliano Bonomi; Jeff Holst; Avner Schlessinger (PLoS Comput. Biol., 2015)

Integrative structural and dynamical biology with PLUMED-ISDB. - Massimiliano Bonomi; Carlo Camilloni (Bioinform., 2017)

What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data? - James S. Fraser; Kresten Lindorff-Larsen; Massimiliano Bonomi (J. Chem. Inf. Model., 2020)

HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design. - Francesco P. Panei; Rachel Torchet; Hervé Ménager; Paraskevi Gkeka; Massimiliano Bonomi (Bioinform., 2022)

Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference. - Samuel E. Hoff; F. Emil Thomasen; Kresten Lindorff-Larsen; Massimiliano Bonomi (PLoS Comput. Biol., 2024)