Folding of RNA has been vastly studied by free energy landscapes which provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions.The kinetics of folding of RNA is limited by length of the RNA molecule. Higher abstraction levels based on a macro-state decomposition of the landscape enable the study of larger systems, however, they are still restricted by huge memory requirements of exact approaches. The approach is evaluated on RNA secondary structure landscapes using a gradient basin definition for macro-states. Furthermore, the authors demonstrate the need for exact transition models by comparing two barrier-based approaches,and perform a detailed investigation of gradient basins in RNA energy landscapes
The new software RNApour works out folding energy barriers in less time and using less memmory. The software is available at the
following URL:https://github.com/ViennaRNA/pourRNA
Reference:
Entzian G. et al.(2020) pour RNA- a time and memmory effecient approach for the guided exploration of RNA energy landcape. Bioinformatics 36(2):462-469.