RNA Structure Modeling Using Physics and Sequence Comparison

Abstract: RNA sequences have pervasive roles in biology and RNA molecules are also important pharmaceuticals. Many of these RNA molecules function by use of specific structures, and these structures are therefore conserved across evolution. With the availability of high throughput methods to identify RNA transcripts and probe structure, there is a need to model these structures to get the most information from available data. The goal of the Mathews lab is to develop algorithms and software to model RNA structures, including secondary and tertiary structures. We focus on using biophysical principles, and we are also at the forefront of incorporating additional information in our models, including experimental mapping data and structure conservation. Here, we will build on the foundation of prior work to develop new structure prediction methods. We provide our software freely to the community and we rigorously test our methods with close collaborations with experimentalists.