Publications by authors named "Simone Marsili"

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Structural insights into MERS and SARS coronavirus membrane proteins.
Mandeep Kaur Mann, Yanting Yin, Simone Marsili, Jiexiong Xie, Jordi Doijen

Commun Biol· November 2025

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A New Fragment-Based Pharmacophore Virtual Screening Workflow Identifies Potent Inhibitors of SARS-CoV-2 NSP13 Helicase.
Jordi Doijen, Jiexiong Xie, Simone Marsili, Trpta Bains, Mandeep Kaur Mann

J Comput Chem· September 2025

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Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy.
Sudarshan Behera, David F Hahn, Carter J Wilson, Simone Marsili, Gary Tresadern

J Chem Inf Model· July 2025

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A small-molecule SARS-CoV-2 inhibitor targeting the membrane protein.
Ellen Van Damme, Pravien Abeywickrema, Yanting Yin, Jiexiong Xie, Sofie Jacobs, Simone Marsili

Nature· April 2025

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Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone.
Juan Rodriguez-Rivas, Simone Marsili, David Juan, Alfonso Valencia

Proc Natl Acad Sci U S A· December 2016

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Correction to "Free Energy Reconstruction in Bidirectional Force Spectroscopy Experiments: The Effect of the Device Stiffness".
Simone Marsili, Piero Procacci

J Phys Chem B· July 2016

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Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs.
David Juan, Juliane Perner, Enrique Carrillo de Santa Pau, Simone Marsili, David Ochoa

Cell Rep· February 2016

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From residue coevolution to protein conformational ensembles and functional dynamics.
Ludovico Sutto, Simone Marsili, Alfonso Valencia, Francesco Luigi Gervasio

Proc Natl Acad Sci U S A· November 2015

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Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones.
Duccio Malinverni, Simone Marsili, Alessandro Barducci, Paolo De Los Rios

PLoS Comput Biol· June 2015

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Energy-Driven Undocking (EDU-HREM) in Solute Tempering Replica Exchange Simulations.
Piero Procacci, Marco Bizzarri, Simone Marsili

J Chem Theory Comput· January 2014

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Insights into the conformational switching mechanism of the human vascular endothelial growth factor receptor type 2 kinase domain.
Matteo Chioccioli, Simone Marsili, Claudia Bonaccini, Piero Procacci, Paola Gratteri

J Chem Inf Model· February 2012

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Conformational structure of the MOG-derived peptide 101-108 in solution.
Carlo Guardiani, Simone Marsili, Stefania Marchetti, Cecilia Gambi, Piero Procacci

Biopolymers· September 2011

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Intraligand hydrophobic interactions rationalize drug affinities for peptidyl-prolyl cis-trans isomerase protein.
Marco Bizzarri, Simone Marsili, Piero Procacci

J Phys Chem B· May 2011

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ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.
Simone Marsili, Giorgio Federico Signorini, Riccardo Chelli, Massimo Marchi, Piero Procacci

J Comput Chem· April 2010

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Free energy reconstruction in bidirectional force spectroscopy experiments: the effect of the device stiffness.
Simone Marsili, Piero Procacci

J Phys Chem B· February 2010

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Fragment 101-108 of myelin oligodendrocyte glycoprotein: a possible lead compound for multiple sclerosis.
Carlo Guardiani, Simone Marsili, Piero Procacci, Roberto Livi

J Am Chem Soc· December 2009

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Thermodynamics of stacking interactions in proteins.
Simone Marsili, Riccardo Chelli, Vincenzo Schettino, Piero Procacci

Phys Chem Chem Phys· May 2008

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Calculation of the potential of mean force from nonequilibrium measurements via maximum likelihood estimators.
Riccardo Chelli, Simone Marsili, Piero Procacci

Phys Rev E Stat Nonlin Soft Matter Phys· March 2008

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Numerical verification of the generalized Crooks nonequilibrium work theorem for non-Hamiltonian molecular dynamics simulations.
Riccardo Chelli, Simone Marsili, Alessandro Barducci, Piero Procacci

J Chem Phys· July 2007

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Generalization of the Jarzynski and Crooks nonequilibrium work theorems in molecular dynamics simulations.
Riccardo Chelli, Simone Marsili, Alessandro Barducci, Piero Procacci

Phys Rev E Stat Nonlin Soft Matter Phys· May 2007

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Recovering the Crooks equation for dynamical systems in the isothermal-isobaric ensemble: a strategy based on the equations of motion.
Riccardo Chelli, Simone Marsili, Alessandro Barducci, Piero Procacci

J Chem Phys· January 2007

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Crooks equation for steered molecular dynamics using a Nosé-Hoover thermostat.
Piero Procacci, Simone Marsili, Alessandro Barducci, Giorgio F Signorini, Riccardo Chelli

J Chem Phys· October 2006

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Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations.
Simone Marsili, Alessandro Barducci, Riccardo Chelli, Piero Procacci, Vincenzo Schettino

J Phys Chem B· July 2006

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