Monte Carlo Energy Landscape Paving and Basin Paving simulation of RNA T-loop hairpin

Conformational landscape of RNA T-loop hairpin has been investigated by Energy Landscape Paving (ELP) and Basin Paving (BP) Monte Carlo simulations. Both ELP and BP simulations use memory of the simulation to increase the probability of the states less visited. The unfolded structures of the RNA were obtained from the folded one by ELP method. Structures were folded from extended structures by BP method. Choice of different parameters, including the use of the end-to-end distance of RNA as a memory term, in the simulations to accelerate sampling is discussed. It has been found that both ELP and BP are highly efficient techniques for unfolding and folding RNA T-loop hairpin.