Table 1.
Quality of predicted RNA 3D modelsa
| RNA PDB code and chain | Strand length (nt) | Accuracyb |
Precisionc | ||
|---|---|---|---|---|---|
| r.m.s.d. (Å) | INFall | INFcbp | r.m.s.d. (Å) | ||
| Hairpin | |||||
| 2DR8 B | 33 | 1.7 | 0.88 | 1.00 | 1.4 |
| 3OVA C | 34 | 3.2 | 0.79 | 1.00 | 2.0 |
| Hairpin, internal loop | |||||
| 1JBR D | 31 | 4.4 | 0.74 | 0.98 | 2.7 |
| 2HW8 B | 36 | 2.8 | 0.86 | 1.00 | 1.4 |
| 1ZHO B | 38 | 2.0 | 0.83 | 0.99 | 1.1 |
| 3IAB R | 46 | 11.0 | 0.72 | 0.88 | 1.2 |
| Hairpin, internal loops | |||||
| 1I6U C | 37 | 2.7 | 0.79 | 0.99 | 2.0 |
| 2PXL B | 47 | 2.3 | 0.84 | 1.00 | 2.1 |
| 2VPL B | 48 | 4.7 | 0.81 | 0.97 | 1.7 |
| 2PXB B | 49 | 3.7 | 0.84 | 1.00 | 2.1 |
| 1MZP B | 55 | 2.5 | 0.78 | 0.99 | 1.7 |
| 1KXK A | 70 | 9.7 | 0.75 | 0.97 | 5.0 |
| Three-way junction | |||||
| 1DK1 B | 57 | 4.1 | 0.82 | 0.98 | 2.4 |
| 1MMS C | 58 | 3.1 | 0.73 | 0.97 | 2.3 |
| 1UN6 E | 61 | 4.0 | 0.80 | 0.88 | 2.2 |
| Three-way junction (hammerhead) | |||||
| 2QUS A | 69 | 3.8 | 0.81 | 0.96 | 1.6 |
| Three-way junction (riboswitch) | |||||
| 3LA5 A | 71 | 1.9 | 0.87 | 1.00 | 1.0 |
| 3D2V A | 77 | 3.3 | 0.82 | 0.99 | 2.0 |
| Three-way junction (GMP riboswitch) | |||||
| 3IWN A | 93 | 3.9 | 0.75 | 0.97 | 2.3 |
| Three-way junction (SRP) | |||||
| 2V3C M | 96 | 10.0 | 0.76 | 0.94 | 3.0 |
| 1LNG B | 97 | 6.6 | 0.77 | 0.99 | 2.6 |
| 1Z43 A | 101 | 4.8 | 0.76 | 0.98 | 2.7 |
| 3NDB M | 136 | 7.2 | 0.80 | 0.96 | 4.2 |
| Three-way junction (5S rRNA) | |||||
| 3OFQ B | 117 | 4.0 | 0.75 | 0.90 | 2.3 |
| 3OFR B | 118 | 4.1 | 0.83 | 1.00 | 3.2 |
| 3KIR B | 119 | 5.1 | 0.77 | 0.94 | 4.4 |
| 3I9E B | 120 | 5.0 | 0.81 | 0.96 | 3.3 |
| 1VQO 9 | 122 | 3.3 | 0.84 | 1.00 | 2.6 |
| Four-way junction (tRNA) | |||||
| 1EXD B | 73 | 2.9 | 0.77 | 1.00 | 2.3 |
| 1U0B A | 74 | 7.1 | 0.69 | 0.99 | 2.5 |
| 1FFY T | 75 | 2.1 | 0.82 | 0.96 | 1.4 |
| 2J00 W | 76 | 3.2 | 0.73 | 0.95 | 2.2 |
| Four-way junction (riboswitch) | |||||
| 3IQP A | 94 | 3.1 | 0.81 | 0.99 | 2.2 |
| Five-way junction (tRNA) | |||||
| 3AM1 B | 81 | 5.4 | 0.78 | 0.99 | 3.9 |
| 1WZ2 C | 88 | 20.5 | 0.66 | 1.00 | 5.1 |
| 3ADB C | 92 | 4.7 | 0.67 | 1.00 | 2.8 |
| Pseudoknot | |||||
| 2QWY A | 52 | 11.2 | 0.54 | 0.98 | 2.2 |
| Pseudoknot (HDV ribozyme) | |||||
| 1CX0 B | 72 | 2.7 | 0.83 | 0.97 | 1.6 |
| P4–P6 ribozyme domain | |||||
| 2R8S R | 159 | 15.2 | 0.76 | 0.99 | 7.9 |
| M-box riboswitch | |||||
| 3PDR A | 161 | 3.2 | 0.81 | 1.00 | 1.3 |
aUpon validation, all the 3D structure elements comprised by the respective crystal PDB structure were excluded from the dictionary.
bDescribed as the average heavy-atom r.m.s.d. (in Å) between 10 individual 3D models and the crystal structure, and the average interaction network fidelity (INF) measures (33). INF scores range from 0.00 (worst) to 1.00 (best).
cDescribed as the average heavy-atom r.m.s.d. (in Å) between 10 individual 3D models predicted and their mean coordinate values.