Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation. - Mattia Falconi; Ruggero Gallimbeni; Emanuele Paci (J. Comput. Aided Mol. Des., 1996)

CHARMM: The biomolecular simulation program. - Bernard R. Brooks; Charles L. Brooks III; Alexander D. MacKerell Jr.; Lennart Nilsson; Robert J. Petrella; Benoît Roux; Y. Won; G. Archontis; Christian Bartels; Stefan Boresch; Amedeo Caflisch; Leo S. D. Caves; et al. (J. Comput. Chem., 2009)

Probing the free energy landscape of the FBP28WW domain using multiple techniques. - Xavier Periole; Lucy R. Allen; Kamil Tamiola; Alan E. Mark; Emanuele Paci (J. Comput. Chem., 2009)

Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations. - Lucy R. Allen; Sergei V. Krivov; Emanuele Paci (PLoS Comput. Biol., 2009)

Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin. - Giovanni Settanni; David Serquera; Piotr E. Marszalek; Emanuele Paci; Laura S. Itzhaki (PLoS Comput. Biol., 2013)

ALMOST: An all atom molecular simulation toolkit for protein structure determination. - Biao Fu; Aleksandr B. Sahakyan; Carlo Camilloni; Gian Gaetano Tartaglia; Emanuele Paci; Amedeo Caflisch; Michele Vendruscolo; Andrea Cavalli (J. Comput. Chem., 2014)

Optimal Reaction Coordinate as a Biomarker for the Dynamics of Recovery from Kidney Transplant. - Sergei V. Krivov; Hayley Fenton; Paul J. Goldsmith; Rajendra K. Prasad; Julie Fisher; Emanuele Paci (PLoS Comput. Biol., 2014)

Assessment of ab initio models of protein complexes by molecular dynamics. - Filip Radom; Andreas Plückthun; Emanuele Paci (PLoS Comput. Biol., 2018)