Table 3.
Identification of peptide binding core by molecular docking and DS-QM.
|
Peptide bound to HLA-DP2 |
Binding mode Binding core is given in bold |
AutoDock FBE (kcal/mol) |
DS-QMnap p1p6 binding score |
|---|---|---|---|
| pdb code: 3lqz | RKFHYLPFLPSTGGS | 9.43 | -0.174 |
| RKFHYLPFLPSTGGS | 8.53 | -10.183 | |
| Binding core | RKFHYLPFLPSTGGS | -5.36 | 0.314 |
| RKFHYLPFLPSTGGS | 6.36 | -0.093 | |
| RKFHYLPFLPSTGGS | 6.69 | -9.043 | |
| RKFHYLPFLPSTGGS | 3.06 | -0.231 | |
| RKFHYLPFLPSTGGS | 3.72 | -0.685 | |
| Apolipoprotein A-II 12-27 | LQSLVSQYFQTVADYA | 0.26 | -0.231 |
| LQSLVSQYFQTVADYA | -0.5 | -0.189 | |
| LQSLVSQYFQTVADYA | -0.36 | -0.218 | |
| Binding core | LQSLVSQYFQTVADYA | 4.54 | 0.073 |
| LQSLVSQYFQTVADYA | -1.75 | -0.171 | |
| LQSLVSQYFQTVADYA | 2.48 | -0.451 | |
| Cathepsin S 182-197 | GGFMTTAFQYIIDNKG | -0.09 | -0.451 |
| GGFMTTAFQYIIDNKG | 0.26 | -0.42 | |
| Binding core | GGFMTTAFQYIIDNKG | -5.99 | 0.314 |
| GGFMTTAFQYIIDNKG | -2.91 | -0.162 | |
| GGFMTTAFQYIIDNKG | 3.79 | -0.148 | |
| GGFMTTAFQYIIDNKG | 3.04 | -0.278 | |
| GGFMTTAFQYIIDNKG | 1.03 | -0.275 | |
| GGFMTTAFQYIIDNKG | -4.91 | -0.098 | |
| Igλ 188-204 | QSNNKYAASSYLSLTPE | 1.42 | -0.055 |
| QSNNKYAASSYLSLTPE | -1.86 | -0.42 | |
| QSNNKYAASSYLSLTPE | 0.4 | -0.308 | |
| QSNNKYAASSYLSLTPE | -0.15 | -0.356 | |
| QSNNKYAASSYLSLTPE | -0.87 | -0.33 | |
| Binding core | QSNNKYAASSYLSLTPE | -5.06 | 0.157 |
| QSNNKYAASSYLSLTPE | -0.3 | -0.271 | |
| QSNNKYAASSYLSLTPE | -2.81 | -0.395 | |
| QSNNKYAASSYLSLTPE | 0.09 | -0.344 | |
| Interferon-induced protein 1-8D 53-65 | VPDHVVWSLFNTL | -4.92 | -0.196 |
| VPDHVVWSLFNTL | -1.81 | -0.746 | |
| VPDHVVWSLFNTL | -3.19 | -0.511 | |
| VPDHVVWSLFNTL | -3.28 | -0.093 | |
| Binding core | VPDHVVWSLFNTL | -6.19 | 0.017 |
| LR11 mosaic ptorein | VYGIFYATSFLDLYRNP | -2.48 | -0.037 |
| VYGIFYATSFLDLYRNP | -1.49 | -0.045 | |
| VYGIFYATSFLDLYRNP | -3.97 | -0.451 | |
| VYGIFYATSFLDLYRNP | -1.38 | -0.249 | |
| Binding core | VYGIFYATSFLDLYRNP | -5.98 | 0.314 |
| VYGIFYATSFLDLYRNP | 2.11 | 0.031 | |
| VYGIFYATSFLDLYRNP | 7.07 | -0.503 | |
| VYGIFYATSFLDLYRNP | 2.12 | -0.274 | |
| VYGIFYATSFLDLYRNP | -3.66 | -0.218 |
The FBE values and the binding scores of the identified binding cores are given in bold.