A New Method to Predict RNA Secondary Structure Based on RNA Folding Simulation

RNA plays an important role in various biological processes; hence, it is essential when determining the functions of RNA to research its secondary structures. So far, the accuracy of RNA secondary structure prediction remains an area in need of improvement. This paper presents a novel method for predicting RNA secondary structure based on an RNA folding simulation model. This model assumes that the process of RNA folding from the random coil state to full structure is staged and in every stage of folding, the final state of an RNA is determined by the optimal combination of helical regions, which are urgently essential to dynamics of RNA formation. This paper proposes the First Large Free Energy Difference (FLED) in order to find the helical regions most urgently needed for optimal final state formation among all the possible helical regions. Tests on the datasets with known structures from public databases demonstrate that our method can outperform other current RNA secondary structure prediction methods in terms of prediction accuracy.