6 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…
The need to implement FAIR principles in biomolecular simulations
Rommie Amaro, Johan à qvist, 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…
Integrating experimental data with molecular simulations to investigate RNA structural dynamics
Mattia Bernetti, Giovanni Bussi
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scatter…
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…