Davide Branduardi
Davide Branduardi
Applications Scientist, Schrödinger Inc
Verified email at schrodinger.com - Homepage
TitleCited byYear
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
10232009
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
9152014
From to in free energy space
D Branduardi, FL Gervasio, M Parrinello
The Journal of chemical physics 126 (5), 054103, 2007
3352007
Metadynamics with adaptive Gaussians
D Branduardi, G Bussi, M Parrinello
Journal of chemical theory and computation 8 (7), 2247-2254, 2012
1282012
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
1192009
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, 2008
1112008
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
972005
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
932008
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, 2011
582011
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
572008
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
542012
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
442013
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
412010
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
362011
Free-energy calculations with metadynamics: Theory and practice
G Bussi, D Branduardi
Rev. Comput. Chem 28, 1-49, 2015
332015
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
282011
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
232009
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
212012
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
192013
A chirality‐based metrics for free‐energy calculations in biomolecular systems
A Pietropaolo, D Branduardi, M Bonomi, M Parrinello
Journal of computational chemistry 32 (12), 2627-2637, 2011
172011
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Articles 1–20