- Abstract Protein-RNA interactions, mediated through both RNA sequence and structure, play vital role in all cellular processes. In recent years, technologies have been developed to measure these interactions in high-throughput manner. Researchers would like to infer accurate models from the experimental data in order to predict new interactions and better understand the underlying binding mechanism. In this tutorial, I will present the main computational challenges in incorporating RNA structure information into computational algorithms and models. I will describe in detail two state-of-the-art methods to infer structure- based models from experimental data and discuss their strengths and weakness. I will conclude with open problems in the field.