RNA Dynamics and Interactions Revealed through Atomistic Simulations

TL;DR

This review discusses how atomistic molecular dynamics simulations, enhanced sampling, and AI are advancing our understanding of RNA conformational dynamics and interactions in various biological contexts.

Contribution

It provides a comprehensive overview of recent methodological advances and the integration of AI in RNA simulation studies.

Findings

Enhanced sampling techniques improve structural ensemble accuracy

AI accelerates RNA modeling and simulation

Simulations reveal detailed RNA conformational dynamics

Abstract

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 characterize RNA dynamics in diverse contexts, including isolated molecules and complexes with ions, small molecules, or proteins. We highlight how enhanced sampling techniques and integrative approaches can improve both the precision and accuracy of the resulting structural ensembles. Finally, we examine the emerging role of artificial intelligence in accelerating progress in RNA modeling and simulation.