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

Ig╬╗ 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.

Patronov et al. BMC Structural Biology 2011 11:32   doi:10.1186/1472-6807-11-32

Open Data