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Proceedings of the National Academy of Sciences of the United States of America|October 22, 2015
From residue coevolution to protein conformational ensembles and functional dynamicsLudovico Sutto, Simone Marsili, Alfonso Valencia, et al.Journal of Chemical Information and Modeling|January 11, 2012
Insights into the conformational switching mechanism of the human vascular endothelial growth factor receptor type 2 kinase domainMatteo Chioccioli, Simone Marsili, Claudia Bonaccini, et al.Plos Computational Biology|June 6, 2015
Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 ChaperonesDuccio Malinverni, Simone Marsili, Alessandro Barducci, et al.The Journal of Physical Chemistry. B|July 21, 2006
Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculationsSimone Marsili, Alessandro Barducci, Riccardo Chelli, et al.Journal of Computational Chemistry|October 14, 2009
ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic levelSimone Marsili, Giorgio Federico Signorini, Riccardo Chelli, et al.The Journal of Chemical Physics|November 10, 2006
Crooks equation for steered molecular dynamics using a Nosé-Hoover thermostatPiero Procacci, Simone Marsili, Alessandro Barducci, et al.Biopolymers|June 16, 2010
Conformational structure of the MOG-derived peptide 101-108 in solutionCarlo Guardiani, Simone Marsili, Stefania Marchetti, et al.Journal of Chemical Theory and Computation|March 4, 2026
Exploring the Structural Basis of Cryptic Pocket Formation Driven by Extensive Protein Conformational Changes in Drug TargetsMartijn P Bemelmans, Alberto Borsatto, Simone Marsili, et al.Journal of Chemical Information and Modeling|June 30, 2025
Quantification of the Impact of Structure Quality on Predicted Binding Free Energy AccuracySudarshan Behera, David F Hahn, Carter J Wilson, et al.Cell Reports|February 3, 2016
Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCsDavid Juan, Juliane Perner, Enrique Carrillo de Santa Pau, et al.Pageof 3