DSSS - Computational Modeling of 3D Structures, Interactions, and Modifications of ncRNAs

Non-coding RNAs (ncRNAs) are important regulators of cellular processes. Their ability to adopt specific three-dimensional structures and interact with proteins, small molecules, and ions underlies functions such as gene regulation, catalysis, and molecular recognition. Understanding these functions requires characterization of both RNA structure and conformational dynamics, as well as the effects of molecular partners on folding and interactions. An additional layer of complexity arises from post-transcriptional RNA modifications, which can influence RNA structure, dynamics, and interactions.
Experimental characterization of RNA structure and dynamics remains challenging, particularly for flexible or partially disordered systems. Computational modeling provides a complementary approach, although its applicability is often limited by system size, complexity, and sampling requirements.
I will present computational approaches that combine coarse-grained and hybrid modeling to study RNA folding, RNA–protein interactions, and the structural effects of chemical modifications. These approaches are implemented in a set of methods developed in my laboratory for structure prediction, complex formation, motif identification, and model assessment. Together, they enable the prediction and analysis of RNA three-dimensional structures and interactions at different levels of resolution.