Giovanni Bussi

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 37

Top Topics

Molecular Dynamics

Single Molecule

Machine Learning

Top Venues

Journal of chemical theory and computation

Journal of chemical information and modeling

The journal of physical chemistry letters

RNA (New York, N.Y.)

This page only lists publications with an associated author ORCID identifier.

Publications

Bernhard C Thiel, Giovanni Bussi, Simón Poblete, Ivo L Hofacker
Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data. Nucleic acids research (2024)
Ivan Gilardoni, Thorben Fröhlking, Giovanni Bussi
Boosting Ensemble Refinement with Transferable Force-Field Corrections: Synergistic Optimization for Molecular Simulations. The journal of physical chemistry letters 15 (5) (2024)
Valerio Piomponi, Miroslav Krepl, Jiřı Šponer, Giovanni Bussi
Molecular Simulations to Investigate the Impact of N6-Methylation in RNA Recognition: Improving Accuracy and Precision of Binding Free Energy Prediction. The journal of physical chemistry. B (2024)
Ivan Gilardoni, Thorben Fröhlking, Giovanni Bussi
Boosting Ensemble Refinement with Transferable Force-Field Corrections: Synergistic Optimization for Molecular Simulations. The journal of physical chemistry letters (2024)
Nicola Calonaci, Mattia Bernetti, Alisha N Jones, Michael Sattler, Giovanni Bussi
Molecular Dynamics Simulations with Grand-Canonical Reweighting Suggest Cooperativity Effects in RNA Structure Probing Experiments. Journal of chemical theory and computation (2023)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling (2023)
Thorben Fröhlking, Mattia Bernetti, Giovanni Bussi
Simultaneous refinement of molecular dynamics ensembles and forward models using experimental data. The Journal of chemical physics 158 (21) (2023)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling 63 (9) (2023)
Wei-Tse Hsu, Valerio Piomponi, Pascal T Merz, Giovanni Bussi, Michael R Shirts
Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations. Journal of chemical theory and computation (2023)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling 63 (9) (2023)
Wei-Tse Hsu, Valerio Piomponi, Pascal T Merz, Giovanni Bussi, Michael R Shirts
Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations. Journal of chemical theory and computation (2023)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling 63 (9) (2023)
Zhengyue Zhang, Jiřı Šponer, Giovanni Bussi, Vojtěch Mlýnský, Petr Sulc, Chad R Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of chemical information and modeling 63 (9) (2023)
Isabell Louise Grothaus, Giovanni Bussi, Lucio Colombi Ciacchi
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans. Journal of chemical information and modeling 62 (20) (2022)
Thorben Fröhlking, Vojtěch Mlýnský, Michal Janeček, Petra Kührová, Miroslav Krepl, Pavel Banáš, Jiřı Šponer, Giovanni Bussi
Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field. Journal of chemical theory and computation 18 (7) (2022)
Valerio Piomponi, Thorben Fröhlking, Mattia Bernetti, Giovanni Bussi
Molecular Simulations Matching Denaturation Experiments for N 6 -Methyladenosine. ACS central science 8 (8) (2022)
Vojtěch Mlýnský, Michal Janeček, Petra Kührová, Thorben Fröhlking, Michal Otyepka, Giovanni Bussi, Pavel Banáš, Jiřı Šponer
Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications. Journal of chemical theory and computation 18 (4) (2022)
Mattia Bernetti, Giovanni Bussi
Pressure control using stochastic cell rescaling. The Journal of chemical physics 153 (11) (2021)
Sandro Bottaro, Giovanni Bussi, Kresten Lindorff-Larsen
Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations. Journal of the American Chemical Society 143 (22) (2021)
Mattia Bernetti, Kathleen B Hall, Giovanni Bussi
Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles. Nucleic acids research 49 (14) (2021)
Matteo Paloni, Giovanni Bussi, Alessandro Barducci
Arginine multivalency stabilizes protein/RNA condensates. Protein science : a publication of the Protein Society 30 (7) (2021)
Antonio Suma, Lucia Coronel, Giovanni Bussi, Cristian Micheletti
Directional translocation resistance of Zika xrRNA. Nature communications 11 (1) (2020)
Vojtěch Mlýnský, Petra Kührová, Tomáš Kühr, Michal Otyepka, Giovanni Bussi, Pavel Banáš, Jiřı Šponer
Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides. Journal of chemical theory and computation 16 (6) (2020)
Nicola Calonaci, Alisha Jones, Francesca Cuturello, Michael Sattler, Giovanni Bussi
Machine learning a model for RNA structure prediction. NAR genomics and bioinformatics 2 (4) (2020)
Petra Kührová, Vojtěch Mlýnský, Marie Zgarbová, Miroslav Krepl, Giovanni Bussi, Robert B Best, Michal Otyepka, Jiřı Šponer, Pavel Banáš
Correction to "Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions". Journal of chemical theory and computation 16 (1) (2019)
Andrea Cesari, Sandro Bottaro, Kresten Lindorff-Larsen, Pavel Banáš, Jiřı Šponer, Giovanni Bussi
Fitting Corrections to an RNA Force Field Using Experimental Data. Journal of chemical theory and computation 15 (6) (2019)
Petra Kührová, Vojtěch Mlýnský, Marie Zgarbová, Miroslav Krepl, Giovanni Bussi, Robert B Best, Michal Otyepka, Jiřı Šponer, Pavel Banáš
Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions. Journal of chemical theory and computation 15 (5) (2019)
Jiřı Šponer, Giovanni Bussi, Miroslav Krepl, Pavel Banáš, Sandro Bottaro, Richard A Cunha, Alejandro Gil-Ley, Giovanni Pinamonti, Simón Poblete, Petr Jurečka, Nils G Walter, Michal Otyepka
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chemical reviews 118 (8) (2018)
Nils Hildebrand, Monika Michaelis, Nina Wurzler, Zhuo Li, Jonathan D Hirst, András Micsonai, József Kardos, Alejandro Gil-Ley, Giovanni Bussi, Susan Köppen, Massimo Delle Piane, Lucio Colombi Ciacchi
Atomistic Details of Chymotrypsin Conformational Changes upon Adsorption on Silica. ACS biomaterials science & engineering 4 (12) (2018)
Sandro Bottaro, Giovanni Bussi, Scott D Kennedy, Douglas H Turner, Kresten Lindorff-Larsen
Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations. Science advances 4 (5) (2018)
Sandro Bottaro, Giovanni Bussi, Giovanni Pinamonti, Sabine Reißer, Wouter Boomsma, Kresten Lindorff-Larsen
Barnaba: software for analysis of nucleic acid structures and trajectories. RNA (New York, N.Y.) 25 (2) (2018)
Vojtěch Mlýnský, Giovanni Bussi
Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility. The journal of physical chemistry letters 9 (2) (2018)
Ramya Rangan, Massimiliano Bonomi, Gabriella T Heller, Andrea Cesari, Giovanni Bussi, Christopher M Dobson
Determination of Structural Ensembles of Proteins: Restraining vs Reweighting. Journal of chemical theory and computation 14 (12) (2018)
Sandro Bottaro, Pavel Banáš, Jiřı Šponer, Giovanni Bussi
Correction to "Free Energy Landscape of GAGA and UUCG RNA Tetraloops". The journal of physical chemistry letters 9 (7) (2018)
Barira Islam, Petr Stadlbauer, Alejandro Gil-Ley, Guillermo Pérez-Hernández, Shozeb Haider, Stephen Neidle, Giovanni Bussi, Pavel Banas, Michal Otyepka, Jiri Sponer
Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations. Journal of chemical theory and computation 13 (6) (2017)
Richard A Cunha, Giovanni Bussi
Unraveling Mg2+-RNA binding with atomistic molecular dynamics. RNA (New York, N.Y.) 23 (5) (2017)
Giovanni Pinamonti, Jianbo Zhao, David E Condon, Fabian Paul, Frank Noè, Douglas H Turner, Giovanni Bussi
Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models. Journal of chemical theory and computation 13 (2) (2017)