Multiscale RNA modeling with NMR chemical shifts
Computational methods to determine RNA structures and conformational ensembles from NMR data
Non-coding RNAs sample multiple conformational states that are essential to their function. Solution-state NMR has been the primary technique for RNA structure determination, and NMR-derived chemical shifts serve as structural “fingerprints” of RNA conformational state(s).
This work — Kexin’s PhD thesis — developed three computational frameworks that use chemical shifts to model RNA structure and dynamics:
- CS-Fold — chemical-shift-guided de novo RNA secondary-structure prediction.
- CS-BME — probabilistic modeling of RNA conformational ensembles.
- CS-Annotate — chemical-shift-based evaluation of RNA structural models.
Selected publications
- Conditional prediction of RNA secondary structure using chemical shifts · J. Phys. Chem. B (2019).
- Probabilistic modeling of RNA ensembles using NMR chemical shifts · J. Phys. Chem. B (2021).
- CS-Annotate: A tool for using NMR chemical shifts to annotate RNA structure · J. Chem. Inf. Model. (2021).