Table 1.
The test set of peptides restricted by MHC class I molecule HLA-A*0201. We used pMHC complex 2V2W (sequence SLYNTVATL) as a common template for homology modeling. The PDB code, amino acid sequence, the all-atom RMSD between X-ray structure and predicted one by the homology modeling (MODELLER), and the all-atom RMSD between X-ray structure and the most abundant conformation obtained from simulated annealing trials.
| PDB code | Sequence | All-Atom RMSD (Å) to X-ray | |
|---|---|---|---|
| Homology modeling | Simulated annealing | ||
| 1I7U | ALWGFVPVL | 1.65 | 2.12 |
| 1QR1 | IISAVVGIL | 1.35 | 1.45 |
| 1EEY | ILSALVGIV | 1.36 | 1.33 |
| 1EEZ | ILSALVGIL | 1.53 | 1.51 |
| 1S9W | SLLMWITQC | 1.87 | 2.02 |
| 1S9X | SLLMWITQA | 1.92 | 2.04 |
| 1S9Y | SLLMWITQS | 1.74 | 2.26 |
| 1TVB | ITDQVPFSV | 2.01 | 1.62 |
| 1TVH | IMDQVPFSV | 1.87 | 1.87 |
| 2V2X | SLFNTVATL | 2.36 | 2.18 |
| 1S8D | SLANTVATL | 1.02 | 1.11 |
| 1T1W | SLFNTIAVL | 1.20 | 1.26 |
| 1T1X | SLYLTVATL | 1.28 | 1.38 |
| 1T1Y | SLYNVVATL | 1.33 | 1.42 |
| 1T1Z | ALYNTAAAL | 1.18 | 1.42 |
| 1T20 | SLYNTIATL | 1.35 | 1.45 |
| 2C7U | SLFNTIAVL | 1.13 | 1.19 |
| Average | 1.54 | 1.63 | |
| Standard Deviation | 0.37 | 0.37 | |