| PLUMED 2: New feathers for an old bird GA Tribello, M Bonomi, D Branduardi, C Camilloni, G Bussi Computer Physics Communications 185 (2), 604-613, 2014 | 1122 | 2014 |
| PLUMED: A portable plugin for free-energy calculations with molecular dynamics M Bonomi, D Branduardi, G Bussi, C Camilloni, D Provasi, P Raiteri, ... Computer Physics Communications 180 (10), 1961-1972, 2009 | 1110 | 2009 |
| From to in free energy space D Branduardi, FL Gervasio, M Parrinello The Journal of chemical physics 126 (5), 054103, 2007 | 359 | 2007 |
| Metadynamics with adaptive Gaussians D Branduardi, G Bussi, M Parrinello Journal of chemical theory and computation 8 (7), 2247-2254, 2012 | 148 | 2012 |
| Nucleotide-dependent conformational states of actin J Pfaendtner, D Branduardi, M Parrinello, TD Pollard, GA Voth Proceedings of the National Academy of Sciences 106 (31), 12723-12728, 2009 | 123 | 2009 |
| Protein conformational transitions: the closure mechanism of a kinase explored by atomistic simulations A Berteotti, A Cavalli, D Branduardi, FL Gervasio, M Recanatini, ... Journal of the American Chemical Society 131 (1), 244-250, 2009 | 118 | 2009 |
| The role of the peripheral anionic site and cation− π interactions in the ligand penetration of the human AChE gorge D Branduardi, FL Gervasio, A Cavalli, M Recanatini, M Parrinello Journal of the American Chemical Society 127 (25), 9147-9155, 2005 | 104 | 2005 |
| The unfolded ensemble and folding mechanism of the C-terminal GB1 β-hairpin M Bonomi, D Branduardi, FL Gervasio, M Parrinello Journal of the American Chemical Society 130 (42), 13938-13944, 2008 | 96 | 2008 |
| Investigating the Mechanism of Substrate Uptake and Release in the Glutamate Transporter Homologue GltPh through Metadynamics Simulations G Grazioso, V Limongelli, D Branduardi, E Novellino, C De Micheli, ... Journal of the American Chemical Society 134 (1), 453-463, 2012 | 62 | 2012 |
| Conformational changes and gating at the selectivity filter of potassium channels C Domene, ML Klein, D Branduardi, FL Gervasio, M Parrinello Journal of the American Chemical Society 130 (29), 9474-9480, 2008 | 57 | 2008 |
| A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations A Lodola, D Branduardi, M De Vivo, L Capoferri, M Mor, D Piomelli, ... PloS one 7 (2), e32397, 2012 | 56 | 2012 |
| Promoting transparency and reproducibility in enhanced molecular simulations M Bonomi, G Bussi, C Camilloni, GA Tribello, P Banáš, A Barducci, ... Nature methods 16 (8), 670-673, 2019 | 50 | 2019 |
| Discovery of a new class of highly potent inhibitors of acid ceramidase: Synthesis and structure–activity relationship (SAR) D Pizzirani, C Pagliuca, N Realini, D Branduardi, G Bottegoni, M Mor, ... Journal of medicinal chemistry 56 (9), 3518-3530, 2013 | 45 | 2013 |
| Free-energy calculations with metadynamics: Theory and practice G Bussi, D Branduardi Rev. Comput. Chem 28, 1-49, 2015 | 43 | 2015 |
| Free-energy-based methods for binding profile determination in a congeneric series of CDK2 inhibitors J Fidelak, J Juraszek, D Branduardi, M Bianciotto, FL Gervasio The Journal of Physical Chemistry B 114 (29), 9516-9524, 2010 | 41 | 2010 |
| Covalent inhibitors of fatty acid amide hydrolase: a rationale for the activity of piperidine and piperazine aryl ureas G Palermo, D Branduardi, M Masetti, A Lodola, M Mor, D Piomelli, ... Journal of medicinal chemistry 54 (19), 6612-6623, 2011 | 37 | 2011 |
| Methyl phosphate dianion hydrolysis in solution characterized by path collective variables coupled with DFT-based enhanced sampling simulations D Branduardi, M De Vivo, N Rega, V Barone, A Cavalli Journal of chemical theory and computation 7 (3), 539-543, 2011 | 30 | 2011 |
| Theoretical Insights into the Mechanism of Carbon Monoxide (CO) Release from CO‐Releasing Molecules SVC Vummaleti, D Branduardi, M Masetti, M De Vivo, R Motterlini, ... Chemistry–A European Journal 18 (30), 9267-9275, 2012 | 23 | 2012 |
| Ensemble of Transition State Structures for the Cis−Trans Isomerization of N-Methylacetamide YA Mantz, D Branduardi, G Bussi, M Parrinello The Journal of Physical Chemistry B 113 (37), 12521-12529, 2009 | 23 | 2009 |
| String method for calculation of minimum free-energy Paths in Cartesian Space in Freely Tumbling Systems D Branduardi, JD Faraldo-Gómez Journal of chemical theory and computation 9 (9), 4140-4154, 2013 | 20 | 2013 |
