I want to model RNA folding energetics

About this workflow

Calculation of the folding energies and flexibilities of RNA structures is less well-developed than modeling the dominant (usually lowest energy) structure of a molecule. While Ribokit does not yet have a workflow per se, here are some things to try.

Workflow

• For 3D RNA folders, the RNAMake package includes predictive models for estimating free energies of folding of tertiary assembly. Measuring such energetics of folding in large RNAs typically requires tracking multiple transitions, and chemical mapping methods can deconvolve those transitions. The LIFFT package enables likelihood-based analysis of these data.

• For single-molecule force spectroscopists, the HelixMC package allows prediction of mechanical properties of long double-stranded RNA and DNA using base-pair-level models derived from RNA crystallography.

Limitations

• These packages are only recently being tested in blind predictions, and are not well integrated with each other yet.

References

Chou, F.-C., Echols, N., Terwilliger, T.C., and Das, R. (2016)
RNA structure refinement using the ERRASER-Phenix pipeline
Methods in Molecular Biology 1320: 269 - 282. | Paper | Link

Chou, F.-C., Sripakdeevong, P., Dibrov, S.M, Hermann, T., and Das, R. (2013)
Correcting pervasive errors in RNA crystallography through enumerative structure prediction
Nature Methods 10: 74 - 76. | Paper | Link