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.
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J Mol Biol. 2008 May 23;379(1):160-73. Epub 2008 Mar 6.
Folding kinetics of large RNAs.
Geis M, Flamm C, Wolfinger MT, Tanzer A, Hofacker IL, Middendorf M, Mandl C, Stadler PF, Thurner C.