Kinetic and Co-Transcriptional Folding of RNA

Early attempts include Pipas & McMahon (1975), who simply summed over all possible secondary structures and evaluated them with respect to free-energy functions. Biological and thermodynamical principles were then used to advanced free-energy functions to get more accurate predictions, which have been used to great effect in algorithms such as UNAFold (Markham et al. 2008) and RNAfold (Hofacker et al. 1994). Stochastic Context-Free Grammars (SCFGs) have also been used to great effect in programs such as Pfold (Knudsen & Hein 1999, Knudsen & Hein 2003). For a review of RNA secondary structure prediction, see Shapiro et al. (2007) or Gardner & Giegerich (2004).