Exploring RNA Structure Space

RNA can form a structurally diverse set of conformations, which are often functionally relevant. Accurately modelling this high degree of conformational variety remains a computational challenge. In the research paper (PNAS 109(8):2890-2895 (2012)) we demonstrated that using hierarchical natural move Monte Carlo one is able to explore the available conformational space for given RNA systems. Below we present examples to demonstrate the efficiency of the hierarchical Monte Carlo approach and tutorials on how generate the corresponding results. Modelling and design with hierarchical natural moves

1. Small symmetric RNA benchmark

We used a small symmetric RNA to benchmark different methods used to sample RNA. The vidoes below show that by including more move-sets in hierarchical sampling, we improve sampling efficiency: more diverse conformations are quickly explored

2. Large symmetric RNA

Our approach is not restricted to only simpled RNA systems, but can tackle large and complex molecular assemblies as well. Due to the complexity of the system, systematic incorporation of collective motions are essential for sampling a large symmetric RNA. This effect is more pronounced in this case than the previous simpler and smaller RNA where saturation of sampling efficiency was quickly observed with respect to adding sampling degrees of freedom.

3. Tutorial to model the small and large RNA systems

The small system is useful to learn how to define hierarchical move-sets in MOSAICS, whereas the large system gives guidance on setting up applications on the size of the ribosome. Tutorial can be downloaded here.