18.8k citations · 35.1k across the 68 of their papers we have counts for
68 papers
RNA Dynamics and Interactions Revealed through Atomistic Simulations
Olivier Languin-Cattoën, Giovanni Bussi
RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characteriz…
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Gareth A. Tribello, Massimiliano Bonomi, Giovanni Bussi +60
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific p…
MDRefine: a Python package for refining Molecular Dynamics trajectories with experimental data
Ivan Gilardoni, Valerio Piomponi, Thorben Fröhlking +1
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce a…
Characterizing RNA oligomers using Stochastic Titration Constant-pH Metadynamics simulations
Tomas F. D. Silva, Giovanni Bussi
RNA molecules exhibit various biological functions intrinsically dependent on their diverse ecosystem of highly flexible structures. This flexibility arises from complex hydrogen-b…
The need to implement FAIR principles in biomolecular simulations
Rommie Amaro, Johan Åqvist, Ivet Bahar +125
This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necess…
Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction
Valerio Piomponi, Miroslav Krepl, Jiri Sponer +1
N6-methyladenosine (m6A) is a prevalent RNA post-transcriptional modification that plays crucial roles in RNA stability, structural dynamics, and interactions with proteins. The YT…