Table 2.
Comparison of minimum free energy (MFE) and restrained MFE structures to final model structure including pseudoknotted base pairs.a
| MFE | MFE + CM + MA | |||
|---|---|---|---|---|
| 5′ R2 RNA | Sensitivity (%) | PPV (%) | Sensitivity (%) | PPV (%) |
| R2Bm | 52.7 | 57.0 | 90.3 | 87.3 |
| R2Sc | 67.7 | 64.3 | 67.7 | 66.4 |
| R2Ch | 37.8 | 48.5 | 37.8 | 48.5 |
| R2Cpr | 51.1 | 57.4 | 67.8 | 64.8 |
| R2Spy | 74.7 | 72.1 | 72.4 | 71.7 |
a
The sensitivity is the percentage of base pairs in the model structure that also appear in the predicted structure and PPV (positive prediction value) is the percentage of base pairs in the predicted structure that match the model structure. A correct pair could include “slippage” of the calculated paired nucleotides +/- one nucleotide. Chemical modifications (CM) include only strong hits from DMS, CMCT, NMIA, and kethoxal (kethoxal for R2Bm only) and microarray constraints (MA) include strong and moderate binding sites.