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

Khan, Javed Mohammed; Ranganathan, Shoba

doi:10.1186/1745-7580-6-S1-S2

Immunome Research

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

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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