RNAstructure

RNAstructure predicts RNA and DNA secondary structures, RNA–RNA interactions, base pairing probabilities, and oligonucleotide binding affinities using thermodynamic algorithms.

Key Features:

• Unimolecular and Bimolecular Structure Prediction: Predicts secondary structures of single-stranded nucleic acids and RNA–RNA duplexes, including microRNA–mRNA and small RNA–mRNA interactions, with base pairing probability calculations.
• Free Energy and Accessibility Modeling: Calculates equilibrium binding affinities and implements free energy density minimization and pseudo-energy minimization (AccessFold) to account for competition between unimolecular and bimolecular structures using pairing probabilities.

Scientific Applications:

• RNA Interaction and Gene Regulation Analysis: Supports investigation of microRNA-mediated silencing, guide RNA–directed modifications, small nuclear RNA–mediated splicing, and other regulatory RNA–RNA interactions.

Methodology:

RNAstructure applies thermodynamic dynamic programming algorithms to minimize folding free energy, extends modeling to bimolecular interactions through free energy density minimization, and incorporates pseudo-free energy penalties derived from unimolecular pairing probabilities (AccessFold) to improve prediction sensitivity for intermolecular base pairs.