The Kinwalker algorithm performs cotranscriptional folding of RNAs, starting at a
user a specified structure (default: open chain) and ending at the minimum
free energy structure. Folding events are performed between transcription
of additional bases and are regulated by barrier heights between the
source and target structure. Barrier heights can be calculated with
two versions of the Morgan-Higgs heuristic as well as a Barrier Tree based
heuristic, as described in the paper (preprint).
Kinwalker also estimates folding times and produces a sequence of files tracking the folding
process (front_trajectory1.ps, front_trajectory2.ps, ...) at the user's request.
Kinwalker program can be downloaded here.