Modeling RNA duplex dynamics with Gibbs sampling enhances base-pair prediction accuracy and reveals structural activity profiles.

ABSTRACT: The RNA secondary (2D) structure prediction problem consists in determining the set of base pairs that form within an RNA molecule from its sequence. A related task is the RNA hybridization problem, where two RNA strands interact to form a duplex. Thermodynamics-based methods typically rely on experimentally determined energy parameters to compute minimum free energy structures for both single-stranded RNAs and duplexes. Through the Boltzmann distribution, these parameters can be used to estimate base-pairing probabilities. Here, we leverage these probabilities to simulate RNA:RNA interaction dynamics. Inspired by the Ising model, we apply Gibbs sampling to model the stochastic formation and disruption of base pairs over time in RNA duplexes, ultimately deriving a consensus structure. The

SUBMITTER: Chasles S 

PROVIDER: S-EPMC12267985 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature