mRNA plays a crucial role in gene expression. Not only, the native mRNA structure which can be termed as the ground state of mRNA folding plays an important role, but also the secondary structures are important in determining gene expression.Various coarse graining methods are needed to lower the enormous energy landscapes into high density representations such as barrier trees. These methods do not take into account the pseudoknots found in RNA molecule.
Kucharik et al.(2016) have developed a new method which takes into account these pseudoknots. They found that the ground state RNAs with pseudoknots will lead to formation of more pseudoknotted intermediates rather than peudoknot free structures.The algorithm of this study has been compiled in C++.For obtaining source code you can visit the following website http://www.tbi.univie.ac.at/bhg.html
Reference:
Marcel Kucharik et al.(2016) Psudoknots in RNA folding.Bioinformatics 32(2):187-194