| title |
|---|
Research |
RNA molecules are highly dynamic, with functions often influenced by multiple structures. Our computational tools complement experimental approaches to reveal these dynamics and their biological implications. Explore our publications for the latest insights on this topic.
We develop enhanced sampling methods to improve the precision of molecular dynamics (MD) simulations. Additionally, we employ integrative approaches to align computational results with experimental data, including force-field improvements, ensemble refinement, and other advanced techniques. You can start the exploration looking at our reviews in this field.
Using molecular dynamics simulations, we characterize the structures and dynamics of RNA molecules, as well as their interactions with ions, proteins, and small molecules, providing insights into their biological roles. A sort of comprehensive review on the topic is available here.
To scale our studies to larger RNA systems, we utilize bioinformatics tools like secondary structure prediction, enabling us to integrate computational insights into complex biological contexts. A sample application of this approach is here, but you can expect more coming.
We are involved in the development PLUMED, an open-source software widely used for enhanced sampling and integrative methods in molecular dynamics simulations. PLUMED integrates seamlessly with various MD engines, enabling advanced methodologies that are central to our research. Dig more in our PLUMED related papers.