I'm a PhD student working with Dr. Wilma
K. Olson at
the Biopolymer Structure Laboratory
in understanding RNA Conformations, Motifs, and
Folds at the nucleotide base step level using a rigid body parameter formalism implemented in the
3DNA (source, web interface) software
package.
Our current work is focused on three main projects:
a) Development of a rigid body formalism for RNA helical regions
implemented in C++.
b) Sequence dependent deformability of RNA helical regions (Including non-canonical Watson-Crick
base-pairing interactions). Such work can be quite useful
for obtaining accurate models of small helical RNA's, for example microRNA's.
c) Automatic classification of the space of RNA base-pairs, and base-steps
parameters using clustering analysis techniques.