Table 2.
The results for the IsRNA1-predicted RNA 3D structures for RNA-Puzzle challenges using sequences and the native 2D structures as input. The all heavy-atom RMSDs for the best candidates from the top 10% lowest energy structures (column “Best of top 10% structure”) and from the top 5 predictions by IsRNA1 (column “Best of top 5 predictions”) are shown for each challenge. For comparison, the best RMSDs for all the submissions (column “Best of all groups”) and for the Chen group submissions (column “Best of Chen group”) are also given. Predictions with RMSD less than or comparable to (ΔRMSD < 0.5 Å) the best of Chen group are marked in boldface, and those better than or comparable to the best of all the groups are printed in italics.
| Puzzle (PDB id) | Length (nts) | Topology | Best of all groups | Best of Chen group | Best of top 10% structures | Best of top 5 predictions |
|---|---|---|---|---|---|---|
| 1 (3mei) | 46 | stem-loop | 3.41 | 4.33 | 2.33 | 3.12 |
| 2 (3p59)a | 100 | stem-loop | 2.50 | 2.83 | 2.12 | 2.23 |
| 3 (3owz) | 84 | 3-way junction | 7.01 | 7.01 | 5.30 | 5.57 |
| 4 (3v7e)b | 126 | tertiary interaction | 3.35 | 3.35 | 2.43 | 3.35 |
| 5 (4p8z) | 188 | tertiary interaction | 8.97 | 25.61 | 24.54 | 27.23 |
| 6 (4gxy) | 168 | tertiary interaction | 11.60 | 22.13 | 23.94 | 34.22 |
| 7 (4r4p) | 185 | 3-way junction | 20.37 | 23.48 | 14.68 | 16.27 |
| 8 (4l81) | 96 | tertiary interaction | 4.80 | 11.29 | 12.43 | 14.25 |
| 9 (5kpy)c | 71 | tertiary interaction | 6.06 | 6.06 | 4.32 | 5.01 |
| 10 tBox (4lck) | 96 | stem-loop | 6.02 | 13.21 | 9.16 | 14.10 |
| 11 X-ray (5lys) | 57 | stem-loop | 4.99 | 4.99 | 5.75 | 8.33 |
| 12 (4qlm) | 125 | tertiary interaction | 10.06 | 16.06 | 12.15 | 14.99 |
| 13 | 71 | tertiary interaction | 5.55 | 6.55 | 4.67 | 7.61 |
| 14 Bound (5ddp) | 61 | 3-way junction | 5.12 | 7.64 | 6.28 | 6.97 |
| 14 Free (5ddo) | 61 | 3-way junction | 6.89 | 9.36 | 7.66 | 10.13 |
| 15 (5di4) | 68 | 3-way junction | 7.12 | 8.51 | 6.61 | 7.26 |
| 17 (5k7c) | 62 | tertiary interaction | 7.16 | 9.45 | 10.67 | 11.78 |
| 18 (5tpy)d | 71 | tertiary interaction | 3.21 | 3.74 | 2.72 | 3.87 |
| 19 (5t5a) | 62 | 3-way junction | 5.52 | 5.52 | 4.08 | 5.19 |
| 20 (5y85) | 68 | 4-way junction | 4.70 | 13.37 | 11.17 | 13.56 |
| 21 (5nz6) | 41 | pseudoknot | 3.93 | 3.83 | 4.01 | 5.02 |
| Average | 6.59 | 9.92 | 8.43 | 10.48 | ||
: 3D coordinates of the nucleotides in the four inner strands were provided and kept rigid in the simulation.
: template extracted from 3IQP was used for nucleotides 1-48, 87-102, and 113-126.
: template extracted from 3DS7 was used for nucleotides 19-27 and 47-55.
: template extracted from 4PQV was used for nucleotides 1-24 and 42-50.