Computational Studies of RNA structure

RNA structure is a young field, but it is also evolving rapidly from a technical standpoint.   New techniques for solving, analyzing and interpreting RNA structures are vital for continued progress in the field of RNA Biology, and many of these approaches are being developed in our laboratory.  We pioneered a reduced representation for the RNA backbone that facilitated rapid structural analysis and motif discovery, and we then leveraged this approach to create the first programs for accurately modeling RNA into electron density.  We are working to make RNA crystallography easier and more accurate, we are developing new ways to interpret the architectural features of large RNA molecules, and we are finding new approaches to the prediction of structure from sequence.

Reduced representations of the RNA backbone enable accurate modeling into electron density.

Relevant Publications

Arena: Rapid and accurate reconstruction of full atomic RNA structures from coarse-grained models
Zion R Perry, Anna Marie Pyle, Chengxin Zhang
Journal of Molecular Biology 2023 () : 168210
RSCanner: rapid assessment and visualization of RNA structure content
Gandhar Mahadeshwar, Rafael Araujo Tavares, Han Wan, Zion Perry, Anna Marie Pyle
Bioinformatics 2023 (39) :
A unified approach to sequential and non-sequential structure alignment of proteins, RNAs and DNAs
Chengxin Zhang, Anna Marie Pyle
iScience 2022 (25) : 105218
US-align: Universal Structure Alignments of Proteins, Nucleic Acids, and Macromolecular Complexes
Chengxin Zhang, Morgan Shine, Anna Marie Pyle, Yang Zhang
Nat Methods 2022 (19) : 1109–1115
AMIGOS III: Pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids
Morgan Shine, Chengxin Zhang, Anna Marie Pyle
Bioinformatics 2022 (38) : 2937-2939
CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures
Chengxin Zhang, Anna Marie Pyle
Acta Crystallogr D 2022 (78) : 466-471
Discovery of highly reactive self-splicing group II introns within the mitochondrial genomes of human pathogenic fungi
Tianshuo Liu, Anna Marie Pyle
Nucleic Acids Res 2021 (49) : 12422-12432
Visualizing the ai5γ group IIB intron
Srinivas Somarowthu, Michal Legiewicz, Kevin S. Keating and Anna Marie Pyle
Nucleic Acids Res. 2013 (42) : 1947-58
Solving nucleic acid structures by molecular replacement: examples from group II intron studies
Marco Marcia, Elisabeth Humphris-Narayaan, Kevin S. Keating, Srinivas Somarowthu, K. Rajashankar and Anna Marie Pyle
Acta Crystallogr D 2013 (69) : 2174-2185
RCrane: semi-automated RNA model building
Kevin S. Keating and Anna Marie Pyle
Acta Crystallogr D 2012 (68) : 985-995
Discrete RNA libraries from pseudo-torsional space
Elisabeth Humphris-Narayanan and Anna Marie Pyle,
J Mol Biol. 2012 (421) : 6-26
A new way to see RNA
Kevin S, Keating, Elisabeth L. Humphris and Anna Marie Pyle
Q Rev Biophys. 2011 (44) : 433-466