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Table 1 Benchmarking pDOCK with our earlier methodology.

From: pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes

S. No. Allele PDB Peptide Length Peptide Sequence Cα RMSD (Å)
      Previous method pDOCK
MHC-I       
1 HLA-A*1101 1qvo 10 QVPLRPMTYK 0.53 0.24
2 HLA-A*0201 1qr1 9 IISAVVGIL 0.46 0.29
3 HLA-A*0201 1akj 9 ILKEPVHGV 0.87 0.39
4 HLA-A*0201 1i1y 9 YLKEPVHGV 0.70 0.66
5 HLA-A*0201 1i7r 9 FAPGFFPYL 0.59 0.47
6 HLA-A*0201 1i7u 9 ALWGFVPVL 0.32 0.29
7 HLA-A*0201 1oga 9 GILGFVFTL 0.32 0.16
8 HLA-A*0201 1qsf 9 LLFGYPVAV 0.54 0.34
9 HLA-A*0201 1lp9 9 ALWGFFPVL 0.58 0.26
10 HLA-A*0201 1s9y 9 SLLMWITQS 1.09 0.39
11 HLA-A*0201 1hhh 10 FLPSDFFPSV 1.10 0.49
12 HLA-A*0201 1jf1 10 ELAGIGILTV 1.53 0.30
13 HLA-B*0801 1agc 8 GGKKKYQL 0.28 0.23
14 HLA-B*0801 1mi5 9 FLRGRAYGL 0.42 0.37
15 HLA-B*2705 1ogt 9 RRKWRRWHL 0.51 0.18
16 HLA-B*2705 2a83 9 RRRWHRWRL 0.55 0.18
17 HLA-B*3501 2cik 9 KPIVVLHGY 0.74 0.26
18 HLA-B*3508 3bwa 8 FPTKDVAL 0.56 0.26
19 HLA-B*5101 1e27 9 LPPVVAKEI 1.27 0.18
20 HLA-B*5301 1a1m 9 TPYDINQML 0.59 0.28
21 HLA-Cw*0401 1im9 9 QYDDAVYKL 0.49 0.34
22 HLA-G*0101 2dyp 9 RIIPRHLQL 0.43 0.16
23 H2-Db 1fg2 9 KAVYNFATC 0.25 0.19
24 H2-Db 3buy 9 LSLRNPILV 0.63 0.23
25 H2-Db 1yn7 10 SSLENFAAYV 0.62 0.14
26 H2-Db 1jpf 11 SGVENPGGYCL 1.14 0.36
27 H2-Dd 1qo3 10 RGPGRAFVTI 1.49 0.17
28 H2-Kb 1t0m 8 SSIEFARL 0.66 0.21
29 H2-Kb 1vac 8 SIINFEKL 0.32 0.22
30 H2-Kb 1wbz 9 SSYRRPVGI 0.89 0.19
31 H2-Kb 1s7q 9 KAVYNFATM 0.20 0.09
32 H2-Kb 1g7p 9 SRDHSRTPM 0.97 0.17
33 H2-Kd 1vgk 9 SYVNTNMGL 0.86 0.25
34 H2-Kk 1zt1 8 FEANGNLI 0.57 0.45
35 H2-Ld 2e7l 9 QLSPFPFDL 0.37 0.35
MHC-II       
36 HLA-DQB1*0602 1uvq 20 MNLPSTKVSWAAVGGGGSLV 1.09 0.23
37 HLA-DRB1*0301 1a6a 15 PVSKMRMATPLLMQA 0.38 0.30
38 HLA-DRB1*0101 1aqd 14 GSDWRFLRGYHQYA 1.08 0.28
39 HLA-DRB1*0101 1fyt 13 PKYVKQNTLKLAT 0.68 0.23
40 HLA-DRB1*0101 2iam 15 GELIGILNAAKVPAD 0.56 0.24
41 HLA-DRB1*0401 1d5x 6 XXRXXX 0.23 0.11
42 HLA-DRB1*0401 1d5z 7 XXRAXSX 0.33 0.22
43 HLA-DRB1*0401 1d6e 8 XXRXMASX 0.32 0.14
44 HLA-DRB1*0401 1j8h 13 PKYVKQNTLKLAT 0.59 0.20
45 HLA-DRB3*0101 2q6w 11 AWRSDEALPLG 0.54 0.30
46 HLA-DRB5*0101 1fv1 20 NPVVHFFKNIVTPRTPPPSQ 0.88 0.59
47 I-Ad 1iao 14 RGISQAVHAAHAEI 0.81 0.27
48 I-Ak 1iak 13 STDYGILQINSRW 0.42 0.23
49 I-Au 2pxy 11 RGGASQYRPSQ 0.78 0.28
50 I-Ek 1r5v 13 ADLIAYPKAATKF 0.82 0.28
  1. Cα RMSD values are calculated only for the nonamer binding cores (shown in bold) for peptides with more than 9 residues in the X-ray crystal structures. X: Amino acid analogues (chemical mimics). A graphical representation of the results is available in Additional File 2 – Figure S1.
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