Research Associate

Publications

Funnel metadynamics as accurate binding free-energy method
V Limongelli, M Bonomi, M Parrinello
Proceedings of the National Academy of Sciences of the United States of America
(2013)
110
Crystal structure of a eukaryotic phosphate transporter
BP Pedersen, H Kumar, AB Waight, AJ Risenmay, Z Roe-Zurz, BH Chau, A Schlessinger, M Bonomi, W Harries, A Sali, AK Johri, RM Stroud
Nature
(2013)
496
High Selectivity of the γ-Aminobutyric Acid Transporter 2 (GAT-2, SLC6A13) Revealed by Structure-based Approach
A Schlessinger, MB Wittwer, A Dahlin, N Khuri, M Bonomi, H Fan, KM Giacomini, A Sali
The Journal of biological chemistry
(2012)
287
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
Journal of Computational Chemistry
(2011)
32
Assessing the quality of the OPEP coarse-grained force field
A Barducci, M Bonomi, P Derreumaux
J Chem Theory Comput
(2011)
7
Metadynamics
A Barducci, M Bonomi, M Parrinello
Wiley Interdisciplinary Reviews 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

Postdoctoral researcher