energy landscapes
Posts tagged “energy landscapes”.
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.
Co-transcriptional folding and metastable states in riboswitch function
This paper uses NMR spectroscopy to resolve transcription intermediates of the 2'dG riboswitch at single-nucleotide resolution, showing how transcript length and metastable states govern ligand-controlled switching.
Memory-efficient exploration of RNA energy landscapes
This paper revisits the earlier flooding-based landscape methods and adapts them to RNA secondary structures with a local, memory-efficient enumeration strategy.
BarMap and RNA folding on dynamic energy landscapes
BarMap models RNA folding on changing energy landscapes by linking macrostates between landscape snapshots, enabling efficient analysis of co-transcriptional and externally perturbed folding scenarios.