Observations of simple RNA suboptimal structures including pseudoknots suggests that the folding landscape is often funnel shaped

Many RNA structure are known to fold up into complex function structures such as ribosomal RNA, transfer RNA (tRNA), riboswitches, etc. We are currently developing a novel theoretical approach for predicting the base pairing topology of folded RNA structures [1,2], a term known as RNA secondary structure. A good prediction of this base pairing can significantly speed up computation of the full 3D structure of these complex molecules. In recent work, we reported a pseudoknot prediction application using this model [3]. We have now upgraded this application to also predict suboptimal structures. The results of this model suggest that structures like tRNA often have a folding landscape of suboptimal structures that is essentially funnel shaped; similar to what is known to be the case for many simple proteins. This model has also been applied to simple protein structure topology prediction in a similar fashion. [1] Dawson, et al. (2001). \textit{J Theor Biol. }213, 359-386 and 387-412. [2] Dawson, et al. (2006). \textit{Nucleosides, Nucleotides, and Nucleic Acids} 25, 171-189. [3]Dawson, et al. (2007). \textit{PLoS One}, 2, 905.