Kinefold is a software for stochastic folding simulations of nucleic acids on second to minute molecular time scales. Renaturation or co-transcriptional folding paths are simulated at the level of helix formation and dissociation in agreement with the seminal experimental results. Pseudoknots and topologically ‘entangled’ helices (i.e. knots) are efficiently predicted taking into account simple geometrical and topological constraints.
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A. Xayaphoummine, T. Bucher & H. Isambert,
Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots,
Nucleic Acid Res., 33, 605-610 (2005)