SHAPE and chemical probing
Chemical probing experiments (SHAPE, DMS and related methods) report, per nucleotide, how reactive a position is to a reagent, and thus how likely it is to be unpaired. The data do not give a structure. They become useful when they enter a structure prediction as soft constraints, i.e. as pseudo-energies that shift the thermodynamic model toward structures compatible with the measurement.
Two methods papers brought this into ViennaRNA (the comparison of SHAPE-to-pseudo-energy conversions, and the perturbation-vector approach), an application to the BVDV IRES, and the tutorial that walks through folding with reactivities in RNAfold, including what to do with partial data. The glossary covers SHAPE, reactivity and soft constraints.
SHAPE and chemical probing tutorial: folding with reactivities in RNAfold
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 what that means 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...