Secondary and tertiary structure of the BVDV IRES
This post summarizes what SHAPE-guided modeling and 3D analysis reveal about a pseudoknot in the BVDV internal ribosome entry site and why that matters for IRES function.
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Predicting RNA structures from sequence and probing data
This review explains how classical thermodynamic RNA folding models can be improved with chemical probing data, and why that combination remains one of the most reliable routes to biologically useful structure prediction.
SHAPE directed RNA folding with the ViennaRNA Package
This paper shows how SHAPE-guided RNA folding is implemented in the ViennaRNA Package, comparing three widely used strategies for turning nucleotide reactivities into soft constraints that improve thermodynamic structure prediction.