Improved prediction of RNA tertiary structure with insights into native state dynamics

Predicted noncanonical base-pairings in loop D/loop E arm of E. coli 5S rRNA. (A) Comparison of NMR structure (pdb_id 1a4d) of loop D/loop E arm of E. coli 5S rRNA (black) and the best RSIM prediction by score (gray). (B) Noncanonical base pairs appearing in the NMR structure (black), relative position of same bases in best scoring RSIM prediction (gray), best prediction of base pair occurring in top 1% of RSIM predictions by score (red). Only one of the six noncanonical base pairs occurred in the RSIMs best scoring structure, and only two were present in the top 1% of all RSIM predictions by score.