Table 3 Identification of peptide binding core by molecular docking and DS-QM.
From: Peptide binding prediction for the human class II MHC allele HLA-DP2: a molecular docking approach
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 | RKFHYLPFL PSTGGS | 9.43 | -0.174 |
| Â | RKFHYLPFLP STGGS | 8.53 | -10.183 |
Binding core | RKFHYLPFLPS TGGS | -5.36 | 0.314 |
| Â | RKFHYLPFLPST GGS | 6.36 | -0.093 |
| Â | RKFHYLPFLPSTG GS | 6.69 | -9.043 |
| Â | RKFHYLPFLPSTGG S | 3.06 | -0.231 |
| Â | RKFHYLPFLPSTGGS | 3.72 | -0.685 |
Apolipoprotein A-II 12-27 | LQSLVSQYF QTVADYA | 0.26 | -0.231 |
| Â | LQSLVSQYFQ TVADYA | -0.5 | -0.189 |
| Â | LQSLVSQYFQT VADYA | -0.36 | -0.218 |
Binding core | LQSLVSQYFQTV ADYA | 4.54 | 0.073 |
| Â | LQSLVSQYFQTVA DYA | -1.75 | -0.171 |
| Â | LQSLVSQYFQTVAD YA | 2.48 | -0.451 |
Cathepsin S 182-197 | GGFMTTAFQ YIIDNKG | -0.09 | -0.451 |
| Â | GGFMTTAFQY IIDNKG | 0.26 | -0.42 |
Binding core | GGFMTTAFQYI IDNKG | -5.99 | 0.314 |
| Â | GGFMTTAFQYII DNKG | -2.91 | -0.162 |
| Â | GGFMTTAFQYIID NKG | 3.79 | -0.148 |
| Â | GGFMTTAFQYIIDN KG | 3.04 | -0.278 |
| Â | GGFMTTAFQYIIDNK G | 1.03 | -0.275 |
| Â | GGFMTTAFQYIIDNKG | -4.91 | -0.098 |
Igλ 188-204 | QSNNKYAAS SYLSLTPE | 1.42 | -0.055 |
| Â | QSNNKYAASS YLSLTPE | -1.86 | -0.42 |
| Â | QSNNKYAASSY LSLTPE | 0.4 | -0.308 |
| Â | QSNNKYAASSYL SLTPE | -0.15 | -0.356 |
| Â | QSNNKYAASSYLS LTPE | -0.87 | -0.33 |
Binding core | QSNNKYAASSYLSL TPE | -5.06 | 0.157 |
| Â | QSNNKYAASSYLSLT PE | -0.3 | -0.271 |
| Â | QSNNKYAASSYLSLTP E | -2.81 | -0.395 |
| Â | QSNNKYAASSYLSLTPE | 0.09 | -0.344 |
Interferon-induced protein 1-8D 53-65 | VPDHVVWSL FNTL | -4.92 | -0.196 |
| Â | VPDHVVWSLF NTL | -1.81 | -0.746 |
| Â | VPDHVVWSLFN TL | -3.19 | -0.511 |
| Â | VPDHVVWSLFNT L | -3.28 | -0.093 |
Binding core | VPDHVVWSLFNTL | -6.19 | 0.017 |
LR11 mosaic ptorein | VYGIFYATS FLDLYRNP | -2.48 | -0.037 |
| Â | VYGIFYATSF LDLYRNP | -1.49 | -0.045 |
| Â | VYGIFYATSFL DLYRNP | -3.97 | -0.451 |
| Â | VYGIFYATSFLD LYRNP | -1.38 | -0.249 |
Binding core | VYGIFYATSFLDL YRNP | -5.98 | 0.314 |
| Â | VYGIFYATSFLDLY RNP | 2.11 | 0.031 |
| Â | VYGIFYATSFLDLYR NP | 7.07 | -0.503 |
| Â | VYGIFYATSFLDLYRN P | 2.12 | -0.274 |
| Â | VYGIFYATSFLDLYRNP | -3.66 | -0.218 |