Table 1.
Rank of the first structure having a RMSD below 2 Å or 3 Å for the backbone or for the whole peptide considering the three protocols. BB: RMSD values considering the backbone; WP: RMSD values considering the whole peptide; “-“: no structure fulfilling the RMSD criteria; a ratio of the actual conserved hydrogen bonds between the crystal structure and the docked solution of the whole peptide (WP) obtained by IRDL.
| PDB Code | IRDL | SP | SP-Peptide | ||||
|---|---|---|---|---|---|---|---|
| BB | WP | H-Bond Number Ratio a | BB | WP | BB | WP | |
| 1OSZ | 2 | 2 | 1 | - | - | 12 | 2 |
| 2D5W | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| 3CH8 | 1 | 1 | 1 | - | - | 1 | 1 |
| 3DRF | 6 | 1 | 0.9 | 11 | 1 | 32 | 4 |
| 3MMG | 1 | 1 | 1 | - | - | 3 | 2 |
| 3T6B | 67 | 1 | 0.75 | 1 | 1 | - | - |
| 4GRV | 1 | 1 | 0.5 | - | - | 1 | 1 |
| 4GYO | 2 | 2 | 0.86 | 9 | 9 | 9 | 9 |
| 4NNM | 1 | 1 | 0.82 | 1 | 1 | 27 | 1 |
| 4Q6H | 2 | 2 | 0.88 | 1 | 1 | 1 | 1 |
| 4RXH | 36 | 36 | 0.8 | 1 | 1 | - | - |