Table 3.
Comparison of de novo modeling of noncanonical RNA motifs with IsRNA2, IsRNA1, and FARFAR model. The best performance over three models with lowest all heavy-atom RMSD is boldfaced for each case.
| No. | Motif name (PDB id) | Sizea | IsRNA2 | IsRNA1 | FARFARe | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Rankb | RMSDc | INFd | rank | RMSD | INF | rank | RMSD | |||
| 1 | Rev response element high-affinity site (1csl) | 6+7 | 1 | 2.72 | 0.77 | 2 | 2.88 | 0.67 | 2 | 3.95 |
| 2 | Fragment with A-C pairs, SRP helix VI (1d4r) | 6+6 | 3 | 0.65 | 0.90 | 1 | 1.00 | 0.97 | 1 | 1.83 |
| 3 | Fragment with G-G and G-A base pairs, SRP helix VI (1d4r) | 8+8 | 1 | 1.87 | 0.78 | 1 | 2.41 | 0.76 | 3 | 3.27 |
| 4 | UUCG tetraloop (1f7y) | 8 | 1 | 2.60 | 0.71 | 1 | 2.77 | 0.67 | 1 | 1.12 |
| 5 | Kink-turn motif (1jj2) | 7+10 | 2 | 9.05 | 0.52 | 4 | 8.55 | 0.62 | 2 | 8.85 |
| 6 | Helix with A-C base pairs (1kd5) | 8+8 | 2 | 2.73 | 0.79 | 2 | 2.45 | 0.73 | 2 | 2.45 |
| 7 | SRP domain IV (1lnt) | 8+8 | 4 | 1.56 | 0.76 | 2 | 2.89 | 0.75 | 4 | 1.54 |
| 8 | Hook-turn motif (1mhk) | 5+6 | 3 | 3.58 | 0.64 | 4 | 4.99 | 0.46 | 5 | 2.56 |
| 9 | GAGA tetraloop from sarcin-ricin loop (1q9a) | 6 | 2 | 0.74 | 0.91 | 3 | 1.15 | 0.61 | 1 | 0.82 |
| 10 | Loop 8, A-type RNase P (1u9s) | 9 | 2 | 3.08 | 0.80 | 1 | 4.45 | 0.67 | 5 | 1.38 |
| 11 | Pentaloop from conserved region of SARS (1xjr) | 9 | 5 | 2.57 | 0.59 | 2 | 3.70 | 0.56 | 3 | 1.10 |
| 12 | L3, thiamine pyrophosphate riboswitch (2gdi) | 9 | 5 | 2.09 | 0.74 | 1 | 3.05 | 0.56 | 4 | 2.00 |
| 13 | Active site, hammerhead ribozyme (2oeu) | 11+7+5 | 4 | 7.67 | 0.65 | 2 | 6.88 | 0.60 | 4 | 8.64 |
| 14 | Stem C internal loop, L1 ligase (2oiu) | 8+8 | 2 | 1.87 | 0.78 | 5 | 5.68 | 0.43 | 1 | 2.24 |
| 15 | J4a-4b region, metal-sensing riboswitch (2qbz) | 9+9 | 5 | 1.46 | 0.82 | 2 | 3.29 | 0.77 | 3 | 3.71 |
| 16 | P1-L3, SAM-II riboswitch (2qwy) | 50 | 2 | 3.94 | 0.62 | 2 | 9.82 | 0.51 | 5 | 7.40 |
| 17 | J4/5 from P4-P6 domain, Tetrahymena thermophila ribozyme (2r8s) | 7+6 | 3 | 1.54 | 0.90 | 4 | 2.98 | 0.72 | 1 | 1.76 |
| 18 | J5-5a hinge, P4-P6 domain, Tetrahymena ribozyme (2r8s) | 10+9 | 5 | 9.35 | 0.55 | 2 | 9.95 | 0.65 | 3 | 9.99 |
| 19 | Pseudoknot, domain III, CPV internal ribosome entry site (3b31) | 12+8 | 1 | 3.77 | 0.85 | 5 | 3.15 | 0.91 | 4 | 3.55 |
| 20 | G-A base pair (157d) | 5+5 | 4 | 0.86 | 0.92 | 3 | 0.88 | 0.96 | 1 | 1.19 |
| 21 | Helix with U-C base pairs (255d) | 6+6 | 1 | 1.38 | 0.87 | 1 | 1.30 | 0.85 | 2 | 2.10 |
| 22 | Loop E motif, 5S RNA (354d) | 11+11 | 1 | 2.57 | 0.62 | 5 | 7.25 | 0.58 | 2 | 1.64 |
| 23 | Pre-catalytic conformation, hammerhead ribozyme (359d) | 11+8+6 | 2 | 5.34 | 0.66 | 2 | 7.14 | 0.71 | 5 | 8.44 |
| average | 2.65 | 3.17 | 0.75 | 2.48 | 4.29 | 0.68 | 2.78 | 3.54 | ||
a
For RNA motif contained multiple chains, the size (number of nucleotides) for each chain is separated by “+”.
b
The rank of the best prediction from the top five clusters.
c
Lowest all-heavy-atom root-mean-square deviation (in Å) for the best prediction from the top five clusters.
d
INF is the interaction network fidelity59 for all the canonical and noncanonical base-pairing and base-stacking interactions.
e
Since the original predictions of FARFAR are unavailable, the INFs for FARFAR are absent here.