ViennaRNA
Posts tagged “ViennaRNA”.
Musashi binding elements in Zika virus 3'UTR
A comparative analysis of Musashi binding element accessibility in Zika virus and related flavivirus 3' UTRs using thermodynamic RNA structure modeling.
Co-transcriptional riboswitch modeling with ViennaRNA
A landscape-based method for modeling how cotranscriptional folding and ligand binding interact in kinetically controlled riboswitches, illustrated with the 2'dG riboswitch from Mesoplasma florum.
In silico design of ligand-triggered RNA switches
A computational workflow for designing ligand-triggered RNA switches, with emphasis on sequence design, folding kinetics, and candidate prioritization.
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...