Research Associate

Publications

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble
M Deighan, M Bonomi, J Pfaendtner
J Chem Theory Comput
(2012)
8
A chirality‐based metrics for free‐energy calculations in biomolecular systems
A Pietropaolo, D Branduardi, M Bonomi, M Parrinello
J Comput Chem
(2011)
32
Assessing the quality of the OPEP coarse-grained force field
A Barducci, M Bonomi, P Derreumaux
Journal of Chemical Theory and Computation
(2011)
7
Metadynamics
A Barducci, M Bonomi, M Parrinello
WIREs Computational Molecular Science
(2011)
1
Multiple Routes and Milestones in the Folding of HIV-1 Protease Monomer
M Bonomi, A Barducci, FL Gervasio, M Parrinello
PLoS One
(2010)
5
Linking well-tempered metadynamics simulations with experiments.
A Barducci, M Bonomi, M Parrinello
Biophys J
(2010)
98
Enhanced sampling in the well-tempered ensemble.
M Bonomi, M Parrinello
Physical Review Letters
(2010)
104
Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition.
V Limongelli, M Bonomi, L Marinelli, FL Gervasio, A Cavalli, E Novellino, M Parrinello
Proceedings of the National Academy of Sciences
(2010)
107
Multiple Routes and Milestones in the Folding of HIV-1 Protease Monomer
M Bonomi, A Barducci, FL Gervasio, M Parrinello
Biophysical Journal
(2010)
98
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
M Bonomi, D Branduardi, G Bussi, C Camilloni, D Provasi, P Raiteri, D Donadio, F Marinelli, F Pietrucci, RA Broglia, M Parrinello
Computer Physics Communications
(2009)
180

Postdoctoral researcher