Giovanni Bussi

14 papers Journal 14
YearRankTypeTitle / Venue / Authors
2025 J jnl
Characterizing RNA Oligomers Using Stochastic Titration Constant-pH Metadynamics Simulations.
J. Chem. Inf. Model.
Tomás F. D. Silva, Giovanni Bussi
2025 J jnl
Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space.
J. Comput. Chem.
Michal Janecek, Petra Kührová, Vojtech Mlýnský, Petr Stadlbauer, Michal Otyepka, Giovanni Bussi, Jirí Sponer, Pavel Banás
2024 J jnl
Molecular dynamics simulations reveal how vinculin refolds partially unfolded talin rod helices to stabilize them against mechanical force.
PLoS Comput. Biol.
Vasyl V. Mykuliak, Rolle Rahikainen, Neil J. Ball, Giovanni Bussi, Benjamin T. Goult, Vesa P. Hytönen
2023 J jnl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.
J. Chem. Inf. Model.
Zhengyue Zhang, Jirí Sponer, Giovanni Bussi, Vojtech Mlýnský, Petr Sulc, Chad R. Simmons, Nicholas Stephanopoulos, Miroslav Krepl
2022 J jnl
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans.
J. Chem. Inf. Model.
Isabell Louise Grothaus, Giovanni Bussi, Lucio Colombi Ciacchi
2018 J jnl
Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments.
Comput.
Andrea Cesari, Sabine Reißer, Giovanni Bussi
2015 J jnl
Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.
BMC Bioinform.
Francesco Di Palma, Sandro Bottaro, Giovanni Bussi
2014 J jnl
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration.
Entropy
Cameron Abrams, Giovanni Bussi
2014 J jnl
PLUMED 2: New feathers for an old bird.
Comput. Phys. Commun.
Gareth A. Tribello, Massimiliano Bonomi, Davide Branduardi, Carlo Camilloni, Giovanni Bussi
2013 J jnl
Structural Role of Uracil DNA Glycosylase for the Recognition of Uracil in DNA Duplexes. Clues from Atomistic Simulations.
J. Chem. Inf. Model.
Duvan Franco, Jacopo Sgrignani, Giovanni Bussi, Alessandra Magistrato
2009 J jnl
PLUMED: A portable plugin for free-energy calculations with molecular dynamics.
Comput. Phys. Commun.
Massimiliano Bonomi, Davide Branduardi, Giovanni Bussi, Carlo Camilloni, Davide Provasi, Paolo Raiteri, Davide Donadio, Fabrizio Marinelli, Fabio Pietrucci, Ricardo A. Broglia, Michele Parrinello
2009 J jnl
SaX: An open source package for electronic-structure and optical-properties calculations in the GW approximation.
Comput. Phys. Commun.
Layla Martin-Samos, Giovanni Bussi
2008 J jnl
A simple asynchronous replica-exchange implementation
CoRR
Giovanni Bussi
2008 J jnl
Stochastic thermostats: comparison of local and global schemes.
Comput. Phys. Commun.
Giovanni Bussi, Michele Parrinello