Abstract
A method is described for detecting local conformational differences between two 3D structures of the same RNA molecule. These could be distinct 3D structures of the same molecule from the same organism, or homologous molecules from different organisms. In this approach, we detect the variability that exists among the relative translation and rotation operations that are needed to superimpose local neighborhoods after an initial rigid-body global superposition. Each translation and rotation is represented by a three dimensional vector. Thus, we investigate the variability within sets of multivariate data. We demonstrate that the method is able to identify both small- and large-scale conformational changes. Matlab/Octave programs to read RNA 3D structure files and compare structures have been developed and are freely accessible at: https://github.com/BGSU-RNA/ConformationalChange.