Post date: Mar 31, 2016 10:21:38 AM
Together with Sandro Bottaro and Alejandro Gil-Ley, we developed a method that can be used to construct RNA folding trajectories starting from static X-ray pictures. The idea is borrowed from Markov state models and diffusion maps, and uses a measure of structural deviation that we developed for RNA structures. We call this method stop motion modeling, in analogy with the animation technique that produces the impression of motion through juxtaposition of static pictures. Using this method, we characterized the folding pathways of common RNA tetraloops, providing results that can be compared with molecular dynamics trajectories and with experiments.
The work has been accepted for publication on Nucleic Acids Research. A preprint is available on arXiv.