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List of works by Simone Marsili

Calculation of the potential of mean force from nonequilibrium measurements via maximum likelihood estimators

scientific article published on 04 March 2008

Conformational structure of the MOG-derived peptide 101-108 in solution

scientific article published on 01 January 2011

Correction to "Free Energy Reconstruction in Bidirectional Force Spectroscopy Experiments: The Effect of the Device Stiffness".

scientific article published on 7 July 2016

Crooks equation for steered molecular dynamics using a Nosé-Hoover thermostat.

scientific article published in October 2006

Energy-Driven Undocking (EDU-HREM) in Solute Tempering Replica Exchange Simulations

scientific article published in January 2014

Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs

scientific article

Fragment 101-108 of myelin oligodendrocyte glycoprotein: a possible lead compound for multiple sclerosis

scientific article published on 01 December 2009

Free energy reconstruction in bidirectional force spectroscopy experiments: the effect of the device stiffness

scientific article published on 01 February 2010

From residue coevolution to protein conformational ensembles and functional dynamics

scientific article

Generalization of the Jarzynski and Crooks nonequilibrium work theorems in molecular dynamics simulations.

scientific article published on 7 May 2007

Insights into the conformational switching mechanism of the human vascular endothelial growth factor receptor type 2 kinase domain.

scientific article

Intraligand hydrophobic interactions rationalize drug affinities for peptidyl-prolyl cis-trans isomerase protein

scientific article published on 18 April 2011

Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones

scientific article (publication date: June 2015)

New advances in metadynamics

Numerical verification of the generalized Crooks nonequilibrium work theorem for non-Hamiltonian molecular dynamics simulations.

scientific article published in July 2007

ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

scientific article published on 01 April 2010

Recovering the Crooks equation for dynamical systems in the isothermal-isobaric ensemble: a strategy based on the equations of motion

scientific article published in January 2007

Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations

scientific article published on 01 July 2006

Thermodynamics of stacking interactions in proteins.

scientific article published on 9 April 2008

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