Fabrizio Marinelli
Fabrizio Marinelli
Staff Scientist, National Institutes of Health, USA
Verified email at nih.gov - 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
A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations
F Marinelli, F Pietrucci, A Laio, S Piana
PLoS computational biology 5 (8), e1000452, 2009
2592009
Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations
F Pietrucci, F Marinelli, P Carloni, A Laio
Journal of the American Chemical Society 131 (33), 11811-11818, 2009
1302009
Targeting biomolecular flexibility with metadynamics
V Leone, F Marinelli, P Carloni, M Parrinello
Current opinion in structural biology 20 (2), 148-154, 2010
1222010
Metadynamics convergence law in a multidimensional system
Y Crespo, F Marinelli, F Pietrucci, A Laio
Physical Review E 81 (5), 055701, 2010
862010
METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations
X Biarnés, F Pietrucci, F Marinelli, A Laio
Computer Physics Communications 183 (1), 203-211, 2012
722012
Predicting the effect of a point mutation on a protein fold: the villin and advillin headpieces and their Pro62Ala mutants
S Piana, A Laio, F Marinelli, M Van Troys, D Bourry, C Ampe, JC Martins
Journal of molecular biology 375 (2), 460-470, 2008
662008
Atomistic simulations indicate the c-subunit ring of the F1Fo ATP synthase is not the mitochondrial permeability transition pore
W Zhou, F Marinelli, C Nief, JD Faraldo-Gómez
eLife, 2017
472017
Exploring the folding free energy landscape of insulin using bias exchange metadynamics
N Todorova, F Marinelli, S Piana, I Yarovsky
The Journal of Physical Chemistry B 113 (11), 3556-3564, 2009
422009
Optimizing the performance of bias-exchange metadynamics: folding a 48-residue LysM domain using a coarse-grained model
P Cossio, F Marinelli, A Laio, F Pietrucci
The Journal of Physical Chemistry B 114 (9), 3259-3265, 2010
392010
Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions
F Marinelli, JD Faraldo-Gómez
Biophysical Journal 108 (12), 2779-2782, 2015
382015
Sodium recognition by the Na+/Ca2+ exchanger in the outward-facing conformation
F Marinelli, L Almagorb, R Hillerb, M Giladib, D Khananshvilib, ...
Proceedings of the National Academy of Sciences, 2014
362014
Theoretical modeling of vibroelectronic quantum states in complex molecular systems: solvated carbon monoxide, a test case
A Amadei, F Marinelli, M D’Abramo, M D’Alessandro, M Anselmi, ...
The Journal of chemical physics 122 (12), 124506, 2005
342005
Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger
J Liao, F Marinelli, C Lee, Y Huang, JD Faraldo-Gómez, Y Jiang
Nature Structural & Molecular Biology, 2016
332016
Following Easy Slope Paths on a Free Energy Landscape: The Case Study of the Trp-Cage Folding Mechanism
F Marinelli
Biophysical journal 105 (5), 1236-1247, 2013
232013
Two-state dynamics of the SH3–SH2 tandem of Abl kinase and the allosteric role of the N-cap
C Corbi-Verge, F Marinelli, A Zafra-Ruano, J Ruiz-Sanz, I Luque, ...
Proceedings of the National Academy of Sciences 110 (36), E3372-E3380, 2013
212013
Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins
F Marinelli, SI Kuhlmann, E Grell, HJ Kunte, C Ziegler, JD Faraldo-Gómez
Proceedings of the National Academy of Sciences 108 (49), E1285-E1292, 2011
212011
Molecular Description of the Propagation of Chirality from Molecules to Complex Systems: Different Mechanisms Controlled by Hydrophobic Interactions
F Marinelli, A Sorrenti, V Corvaglia, V Leone, G Mancini
Chemistry-A European Journal 18 (46), 14680-14688, 2012
152012
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
132019
The prokaryotic Na+/Ca2+ exchanger NCX_Mj transports Na+ and Ca2+ in a 3: 1 stoichiometry
I Shlosman, F Marinelli, JD Faraldo-Gómez, JA Mindell
The Journal of General Physiology, jgp. 201711897, 2017
92017
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Articles 1–20