SHAPE
Posts tagged “SHAPE”.
SHAPE and chemical probing data in RNA structure prediction: how to fold with reactivities in ViennaRNA
How SHAPE reactivities go into RNAfold, what the three methods in ViennaRNA do with them, and what probing data change in a prediction and what they do not. Worked example with yeast tRNA-Phe, all...
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.
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 ViennaRNA: reactivities as soft constraints
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...