PLUMED: A portable plugin for free-energy calculations with molecular dynamics. - Massimiliano Bonomi; Davide Branduardi; Giovanni Bussi; Carlo Camilloni; Davide Provasi; Paolo Raiteri; Davide Donadio; Fabrizio Marinelli 002; Fabio Pietrucci; Ricardo A. Broglia; Michele Parrinello (Comput. Phys. Commun., 2009)

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations. - Fabrizio Marinelli 002; Fabio Pietrucci; Alessandro Laio; Stefano Piana (PLoS Comput. Biol., 2009)

Exploring the Universe of Protein Structures beyond the Protein Data Bank. - Pilar Cossio; Antonio Trovato; Fabio Pietrucci; Flavio Seno; Amos Maritan; Alessandro Laio (PLoS Comput. Biol., 2010)

METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations. - Xevi Biarnés; Fabio Pietrucci; Fabrizio Marinelli 002; Alessandro Laio (Comput. Phys. Commun., 2012)

Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape. - Andrea Basciu; Giuliano Malloci; Fabio Pietrucci; Alexandre M. J. J. Bonvin; Attilio Vittorio Vargiu (J. Chem. Inf. Model., 2019)

Data-driven path collective variables. - Arthur France-Lanord; Hadrien Vroylandt; Mathieu Salanne; Benjamin Rotenberg; A. Marco Saitta; Fabio Pietrucci (CoRR, 2023)