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Simone Marsili
Simone Marsili
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Anno
Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations
S Marsili, A Barducci, R Chelli, P Procacci, V Schettino
The Journal of Physical Chemistry B 110 (29), 14011-14013, 2006
1432006
New advances in metadynamics
L Sutto, S Marsili, FL Gervasio
Wiley Interdisciplinary Reviews: Computational Molecular Science 2 (5), 771-779, 2012
1382012
From residue coevolution to protein conformational ensembles and functional dynamics
L Sutto, S Marsili, A Valencia, FL Gervasio
Proceedings of the National Academy of Sciences 112 (44), 13567-13572, 2015
1202015
ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level
S Marsili, GF Signorini, R Chelli, M Marchi, P Procacci
Journal of computational chemistry 31 (5), 1106-1116, 2010
922010
Thermodynamics of stacking interactions in proteins
S Marsili, R Chelli, V Schettino, P Procacci
Physical Chemistry Chemical Physics 10 (19), 2673-2685, 2008
832008
Crooks equation for steered molecular dynamics using a Nosé-Hoover thermostat
P Procacci, S Marsili, A Barducci, GF Signorini, R Chelli
The Journal of chemical physics 125 (16), 164101, 2006
712006
Large-scale conformational transitions and dimerization are encoded in the amino-acid sequences of Hsp70 chaperones
D Malinverni, S Marsili, A Barducci, P De Los Rios
PLoS computational biology 11 (6), e1004262, 2015
552015
Epigenomic co-localization and co-evolution reveal a key role for 5hmC as a communication hub in the chromatin network of ESCs
D Juan, J Perner, EC de Santa Pau, S Marsili, D Ochoa, HR Chung, ...
Cell reports 14 (5), 1246-1257, 2016
472016
Generalization of the Jarzynski and Crooks nonequilibrium work theorems in molecular dynamics simulations
R Chelli, S Marsili, A Barducci, P Procacci
Physical Review E 75 (5), 050101, 2007
422007
Calculation of the potential of mean force from nonequilibrium measurements via maximum likelihood estimators
R Chelli, S Marsili, P Procacci
Physical Review E 77 (3), 031104, 2008
362008
Conservation of coevolving protein interfaces bridges prokaryote–eukaryote homologies in the twilight zone
J Rodriguez-Rivas, S Marsili, D Juan, A Valencia
Proceedings of the National Academy of Sciences 113 (52), 15018-15023, 2016
332016
Wiley Interdiscip
L Sutto, S Marsili, FL Gervasio
Rev.: Comput. Mol. Sci 2 (771), 10.1002, 2012
252012
Energy dissipation asymmetry in the non equilibrium folding/unfolding of the single molecule alanine decapeptide
P Procacci, S Marsili
Chemical Physics 375 (1), 8-15, 2010
182010
New perspective on how and why immunophilin FK506-related ligands work
M Bizzarri, E Tenori, MR Martina, S Marsili, G Caminati, S Menichetti, ...
The Journal of Physical Chemistry Letters 2 (22), 2834-2839, 2011
172011
Numerical verification of the generalized Crooks nonequilibrium work theorem for non-Hamiltonian molecular dynamics simulations
R Chelli, S Marsili, A Barducci, P Procacci
The Journal of chemical physics 127 (3), 034110, 2007
172007
Recovering the Crooks equation for dynamical systems in the isothermal-isobaric ensemble: a strategy based on the equations of motion
R Chelli, S Marsili, A Barducci, P Procacci
The Journal of chemical physics 126 (4), 044502, 2007
172007
Free energy reconstruction in bidirectional force spectroscopy experiments: The effect of the device stiffness
S Marsili, P Procacci
The Journal of Physical Chemistry B 114 (7), 2509-2516, 2010
162010
Free energy reconstruction in bidirectional force spectroscopy experiments: The effect of the device stiffness
S Marsili, P Procacci
The Journal of Physical Chemistry B 114 (7), 2509-2516, 2010
162010
Energy-driven undocking (EDU-HREM) in solute tempering replica exchange simulations
P Procacci, M Bizzarri, S Marsili
Journal of Chemical Theory and Computation 10 (1), 439-450, 2014
152014
Intraligand Hydrophobic Interactions Rationalize Drug Affinities for Peptidyl− Prolyl Cis− Trans Isomerase Protein
M Bizzarri, S Marsili, P Procacci
The Journal of Physical Chemistry B 115 (19), 6193-6201, 2011
102011
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Articoli 1–20