SHAPE, DMS, and related probing experiments can sharpen RNA structure analysis substantially, but only if the data are interpreted as evidence with limits rather than as a direct readout of base pairing.
SHAPE data can improve RNA structure prediction substantially, but only when the experiment, the model, and the biological question line up in the right way.
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.
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.
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.