We developed a framework to analyze and RNA structures. The method is based on a coarse-grain representation of RNA, with a single oriented bead per nucleotide. Using this technique we define a scoring function that can be used to classify RNA structures and could be of great usefulness for RNA structure prediction. Notably, this scoring function performs equally or better than more complicated all-atom scoring functions. Additionally, we define a metric to measure structural deviation in RNA that can be used to analyze and annotate effectively experimental structures as well as molecular dynamics trajectories. All the developed tools are available in the open source package baRNAba.
This work has been just accepted for publication on Nucleic Acids Research. A preprint is available at arXiv:1410.1271.