A simple asynchronous replica-exchange implementation - Giovanni Bussi (CoRR, 2008)

Stochastic thermostats: comparison of local and global schemes. - Giovanni Bussi; Michele Parrinello (Comput. Phys. Commun., 2008)

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)

SaX: An open source package for electronic-structure and optical-properties calculations in the GW approximation. - Layla Martin-Samos; Giovanni Bussi (Comput. Phys. Commun., 2009)

Structural Role of Uracil DNA Glycosylase for the Recognition of Uracil in DNA Duplexes. Clues from Atomistic Simulations. - Duvan Franco; Jacopo Sgrignani; Giovanni Bussi; Alessandra Magistrato (J. Chem. Inf. Model., 2013)

PLUMED 2: New feathers for an old bird. - Gareth A. Tribello; Massimiliano Bonomi; Davide Branduardi; Carlo Camilloni; Giovanni Bussi (Comput. Phys. Commun., 2014)

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. - Cameron Abrams; Giovanni Bussi (Entropy, 2014)

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations. - Francesco Di Palma; Sandro Bottaro; Giovanni Bussi (BMC Bioinform., 2015)

Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments. - Andrea Cesari; Sabine Reißer; Giovanni Bussi (Comput., 2018)

Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans. - Isabell Louise Grothaus; Giovanni Bussi; Lucio Colombi Ciacchi (J. Chem. Inf. Model., 2022)

Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. - Zhengyue Zhang; Jirí Sponer; Giovanni Bussi; Vojtech Mlýnský; Petr Sulc; Chad R. Simmons; Nicholas Stephanopoulos; Miroslav Krepl (J. Chem. Inf. Model., 2023)

Molecular dynamics simulations reveal how vinculin refolds partially unfolded talin rod helices to stabilize them against mechanical force. - Vasyl V. Mykuliak; Rolle Rahikainen; Neil J. Ball; Giovanni Bussi; Benjamin T. Goult; Vesa P. Hytönen (PLoS Comput. Biol., 2024)

Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space. - Michal Janecek; Petra Kührová; Vojtech Mlýnský; Petr Stadlbauer; Michal Otyepka; Giovanni Bussi; Jirí Sponer; Pavel Banás (J. Comput. Chem., 2025)

Characterizing RNA Oligomers Using Stochastic Titration Constant-pH Metadynamics Simulations. - Tomás F. D. Silva; Giovanni Bussi (J. Chem. Inf. Model., 2025)