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Davide Branduardi
Davide Branduardi
Computational Chemistry & Informatics Group at Astex
Verified email at astx.com - Homepage
Title
Cited by
Cited by
Year
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
26752014
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
16752009
From A to B in free energy space
D Branduardi, FL Gervasio, M Parrinello
The Journal of chemical physics 126 (5), 2007
5792007
Promoting transparency and reproducibility in enhanced molecular simulations
M Bonomi, G Bussi, C Camilloni, GA Tribello, P Baná¹, A Barducci, ...
Nature methods 16 (8), 670-673, 2019
4022019
Metadynamics with adaptive Gaussians
D Branduardi, G Bussi, M Parrinello
Journal of chemical theory and computation 8 (7), 2247-2254, 2012
2682012
Promoting transparency and reproducibility in enhanced molecular simulations
Nature methods 16 (8), 670-673, 2019
2092019
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
1452009
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
1392009
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
1292005
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
1092008
Free‐energy calculations with metadynamics: Theory and practice
G Bussi, D Branduardi
Reviews in Computational Chemistry Volume 28, 1-49, 2015
1082015
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
742012
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
722012
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
652008
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
562013
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
552010
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
432011
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
412011
Cytostatic and cytotoxic effects of topotecan decoded by a novel mathematical simulation approach
M Lupi, G Matera, D Branduardi, M D’Incalci, P Ubezio
Cancer research 64 (8), 2825-2832, 2004
372004
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
332013
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