Table 1. Graph results for RNAs including k-turn and non k-turn motifs using k-turn versus general potentials.
| K-turn potentials applied | General potentials applied | |||||||
|---|---|---|---|---|---|---|---|---|
| PDB | L | RNA class | P1 (best RMSD) | C1 (best score) | C2 (last graph) | P1 (best RMSD) | C1 (best score) | C2 (last graph) |
| K-turns | ||||||||
| 1E7K_D | 17 | snRNA | 2.64 | 2.70 | 2.76 | 2.63 | 3.16 | 3.15 |
| 3SIU_C | 28 | snRNA | 2.46 | 3.23a | 3.22 | 2.28 | 4.46 | 4.45 |
| 2XEB_AB | 33 | snRNA | 3.73 | 4.37 | 4.37 | 3.61 | 6.27 | 6.05 |
| 2OZB_C | 33 | snRNA | 3.49 | 6.10 | 5.68 | 3.25 | 6.90 | 6.90 |
| 2HW8_B | 36 | mRNA | 2.33 | 3.00 | 3.04 | 2.34 | 7.16 | 6.44 |
| 1ZHO_B | 38 | mRNA | 2.45 | 2.84a | 2.90 | 2.45 | 7.11 | 6.55 |
| 2VPL_B | 48 | mRNA | 2.78 | 3.91 | 3.77 | 2.67 | 7.59 | 7.05 |
| 1U63_B | 49 | mRNA | 2.99 | 4.66 | 4.62 | 2.99 | 9.34 | 6.86 |
| 1MZP_B | 55 | rRNA | 2.68 | 4.66 | 4.62 | 3.70 | 6.72 | 6.60 |
| 2GIS_A | 94 | SAM Ribosw. | 13.58 | 17.87 | 18.07 | 13.45 | 18.31 | 18.52 |
| 3V7E_D | 127 | SAM Ribosw. | 13.15 | 21.17 | 21.23 | 13.15 | 22.26 | 22.30 |
| Non K-turns | ||||||||
| 1RLG_D | 25 | Box C/D RNA | 2.43 | 3.81 | 3.97 | 2.49 | 3.80 | 3.58 |
| 1OOA_D | 29 | Aptamer | 2.65 | 3.76 | 3.15 | 2.65 | 3.76 | 3.15 |
| 2IPY_C | 30 | IRE RNA | 2.01 | 2.22 | 2.18 | 2.01 | 2.22 | 2.18 |
| 1MJI_C | 34 | 5S rRNA | 2.38 | 3.26 | 3.24 | 2.38 | 3.44 | 3.39 |
| 1I6U_D | 37 | rRNA fragment | 1.56 | 2.44 | 2.30 | 1.61 | 2.39 | 2.39 |
| 1F1T_A | 38 | Aptamer | 1.93 | 2.77 | 2.77 | 1.96 | 2.67 | 2.65 |
| 1S03_B | 47 | mRNA | 1.94 | 4.18 | 3.87 | 1.98 | 4.29 | 4.28 |
| 1XJR_A | 47 | Viral RNA | 3.99 | 6.26 | 6.32 | 4.23 | 6.43 | 6.30 |
| 2PXB_B | 49 | SRP | 1.99 | 3.88 | 2.72 | 1.99 | 3.88 | 2.72 |
| 2OIU_P | 51 | Ribozyme ligase | 4.51 | 6.61 | 6.87 | 4.51 | 6.61 | 6.87 |
| 2HGH_B | 55 | 5S rRNA | 4.24 | 6.15 | 6.40 | 4.24 | 6.43 | 6.24 |
| 1DK1_B | 57 | rRNA fragment | 4.42 | 6.76 | 8.67 | 4.42 | 6.73 | 10.43 |
| 1MMS_C | 58 | rRNA fragment | 4.64 | 9.19 | 9.26 | 4.64 | 9.19 | 9.26 |
| 1D4R_AB | 58 | SRP | 5.95 | 8.17 | 7.87 | 5.95 | 8.17 | 7.87 |
| 1KXK_A | 70 | Group II intron | 2.99 | 4.07 | 5.48 | 3.48 | 5.52 | 4.58 |
| 1SJ4_R | 73 | HDV ribozyme | 6.51 | 7.36 | 7.92 | 6.07 | 7.00 | 7.06 |
| 1P5O_A | 77 | HCV IRES | 5.58 | 11.21 | 11.75 | 5.49 | 10.40 | 10.33 |
| 3D2G_A | 77 | TPP ribosw. | 7.16 | 16.81 | 17.05 | 6.06 | 13.11 | 13.46 |
| 2HOJ_A | 79 | TPP ribosw. | 6.63 | 17.24 | 16.24 | 6.63 | 18.06 | 16.85 |
| 2GDI_X | 80 | TPP ribosw. | 7.14 | 18.60 | 19.57 | 7.03 | 17.56 | 17.80 |
| 1LNG_B | 97 | SRP | 5.53 | 14.79 | 17.51 | 5.61 | 15.01 | 13.85 |
| 2LKR_A | 111 | U2/U6 snRNA | 14.25 | 21.82 | 22.32 | 14.25 | 18.20 | 20.66 |
| 1MFQ_A | 128 | SRP | 15.41 | 27.24 | 27.44 | 16.48 | 30.22 | 26.97 |
| 1GID_A | 158 | Group I intron | 14.66 | 26.18 | 25.65 | 14.66 | 25.13 | 26.19 |
aAll-atom models built using our fragment assembly approach (S. Jain and T. Schlick, in preparation) yield RMSDs of 3.62 Å for 3SIU, and 1.89 Å for 1ZHO, with respect to the experimental structures, as sketched in Supplementary Figure S6.
Best RMSDs when the reference structure is not known are indicated in bold in each row. After MC/SA sampling, the lowest graph RMSD with respect to the reference graphs from solved structures (P1), lowest scored graph (C1) and last accepted graph (C2) are shown.