Table 1. Comparison with other methods.
Results from GARN runs with default parameters for full structures were compared with those for iFoldRNA, MCSym, FARNA and NAST. Not all servers can handle the ten structures of the test set, either due to the complexity of sampling or because the fragment templates are not available. For iFoldRNA, the only input provided to the server is the sequence. For NAST, only the secondary structure is used. The results obtained with NAST and iFoldRNA are therefore less accurate than those obtained with other techniques. NAST performs well on molecules of fewer than 50 nucleotides, but information about tertiary interactions is required to improve the results obtained. Our procedure not only yields better overall results for the minimal RMSD structure, it also provides several structures close to that of the native sample to choose from.
| PDB ID | # Nucleotides | # Players | RMSD | GARN | iFoldRNA | MCSym | Farna | NAST |
|---|---|---|---|---|---|---|---|---|
| 1MZP | 55 | 8 | min | 4.32 | 8.23 | NA | 5.61 | 12.97 |
| max | 10.58 | 12.68 | NA | 17.80 | 26.38 | |||
| # of samples with RMSD < 5Å (on 50 samples) | 7 | 0 | – | 0 | 0 | |||
| 1E8O | 49 | 8 | min | 6.82 | 12.62 | 6.75 | 7.78 | 12.34 |
| max | 15.40 | 17.71 | 15.55 | 21.02 | 20.29 | |||
| # of samples with RMSD < 8Å (on 50 samples) | 13 | 0 | 1 | 1 | 0 | |||
| 4FE5 | 67 | 14 | min | 7.14 | 15.04 | NA | 7.80 | 17.00 |
| max | 14.53 | 20.12 | NA | 20.98 | 34.17 | |||
| # of samples with RMSD < 9Å (on 50 samples) | 2 | 0 | – | 1 | 0 | |||
| 4QJH | 74 | 15 | min | 7.87 | 11.34 | NA | 8.99 | 23.44 |
| max | 14.93 | 21.24 | NA | 18.67 | 26.57 | |||
| # of samples with RMSD < 9Å (on 50 samples) | 3 | 0 | – | 1 | 0 | |||
| 4TS0 | 89 | 21 | min | 10.42 | NA | NA | 9.47 | 19.84 |
| max | 23.13 | NA | NA | 23.19 | 22.79 | |||
| # of samples with RMSD < 12Å (on 50 samples) | 4 | – | – | 4 | 0 | |||
| 1LNG | 97 | 16 | min | 7.85 | 11.92 | 10.52 | 12.67 | 36.49 |
| max | 17.07 | 35.53 | 29.58 | 30.19 | 59.66 | |||
| # of samples with RMSD < 10Å (on 50 samples) | 6 | 0 | – | 0 | 0 | |||
| 4WFL | 107 | 18 | min | 8.82 | 18.08 | NA | 11.33 | 43.41 |
| max | 16.22 | 25.75 | NA | 26.00 | 47.04 | |||
| # of samples with RMSD < 10Å (on 50 samples) | 5 | 0 | – | 0 | 0 | |||
| 4QK8 | 124 | 20 | min | 12.25 | 18.66 | NA | 13.23 | 54.43 |
| max | 22.78 | 28.49 | NA | 22.19 | 59.44 | |||
| # of samples with RMSD < 14Å (on 50 samples) | 3 | 0 | – | 1 | 0 | |||
| 1MFQ | 127 | 24 | min | 9.68 | 20.42 | 16.07 | 16.13 | 38.91 |
| max | 20.64 | 34.08 | 30.97 | 41.27 | 44.17 | |||
| # of samples with RMSD < 11Å (on 50 samples) | 7 | 0 | – | 0 | 0 | |||
| 4GXY | 172 | 32 | min | 14.27 | NA | NA | 15.84 | 69.04 |
| max | 31.04 | NA | NA | 26.17 | 74.83 | |||
| # of samples with RMSD < 15Å (on 50 samples) | 2 | 0 | – | 0 | 0 | |||