RNA can form complex 3D shapes, which facilitates interactions with other molecules and gives rise to many important functions of post-transcriptional control. Chemical structure probing methods can identify RNA regions that can be chemically modified and with a modelling input each nucleotide can be predicted as structurally flexible or not. Recent methods can identify the interacting sites of RNA and proteins. The aim is to integrate these data sources in a Hidden Markov Model to see what new information about RNA structure the protein binding provides. The model will be applied within a collaborative project to study Motor Neurone Disease.