Kinetic metric for basins of attraction of RNA secondary structures and analysis of the ultrametricity of the energy landscape

A method for testing the hypothesis of an ultrametric organization of the energy landscape of RNA secondary structures is proposed, based on the analysis of the kinetics of transitions between basins of attraction. The method is based on a kinetic metric constructed from the spectral decomposition of the symmetrized Kramers transition rate matrix and the Mahalanobis distance, and it is not an ultrametric by construction. A computational scheme has been developed that includes automatic filtering of noise eigenmodes and a procedure for analyzing disconnected structure graphs. The performance of the method is demonstrated on a sample of reference and random RNAs.