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

Immunome Research

Table 4 Docking novel peptides onto a single template: pDOCK compared to our previous method.

MHC class	Peptide PDB Allele	Peptide PDB	MHC Template Structure	Template Allele	Peptide Length	Peptide Sequence	Cα RMSD (Å)
							Previous method	pDOCK
I	HLA-A*0201	2v2w	1qrn	HLA-A*0201	9	SLYNTVATL	0.63	0.38
I	HLA-A*0201	1hhh	1qrn	HLA-A*0201	10	FLPSDFFPSV	0.58	0.25
I	HLA-A*0201	1qse	1qrn	HLA-A*0201	9	LLFGYPRYV	0.62	0.30
I	HLA-A*0201	2bnq	1qrn	HLA-A*0201	9	SLLMWITQV	0.97	0.77
I	HLA-A*0201	2gj6	1qrn	HLA-A*0201	9	LLFGKPVYV	0.56	0.24
I	HLA-A*0201	1qr1	1qrn	HLA-A*0201	9	IISAVVGIL	0.87	0.36
I	HLA-A*0201	1qsf	1qrn	HLA-A*0201	9	LLFGYPVAV	0.94	0.41
I	HLA-A*0201	1bd2	1qrn	HLA-A*0201	9	LLFGYPVYV	0.68	0.46
I	HLA-A*0201	1hhg	1i4f	HLA-A*0201	9	TLTSCNTSV	0.58	0.56
I	HLA-A*0201	1hhh	1i4f	HLA-A*0201	10	FLPSDFFPSV	1.48	0.57
I	H2-Kb	1osz	1nam	H2-Kb	8	RGYLYQGL	0.85	0.47
I	H2-Kb	1fo0	1nam	H2-Kb	8	INFDFNTI	0.62	0.35
I	H2-Kb	1g6r	1nam	H2-Kb	8	SIYRYYGL	0.66	0.11
I	H2-Kb	1kbg	1nam	H2-Kb	8	RGYVYXGL	0.40	0.06
I	H2-Kb	1g7p	1nam	H2-Kb	9	SRDHSRTPM	1.41	0.82
II	HLA-DRB1*0101	1fyt	2iam	HLA-DRB1*0101	13	PKYVKQNTLKLAT	0.69	0.35
II	HLA-DRB1*0101	1klu	2iam	HLA-DRB1*0101	15	GELIGTLNAAKVPAD	0.85	0.59
II	HLA-DRB1*0101	1t5w	2iam	HLA-DRB1*0101	13	AAYSDQATPLLLS	0.99	0.65
II	HLA-DRB1*0101	1pyw	2iam	HLA-DRB1*0101	9	FVKQNAXAL	0.40	0.32
II	HLA-DRB1*0101	1sje	2iam	HLA-DRB1*0101	15	PEVIPMFSALSEGAT	0.70	0.37
II	HLA-DRB1*0101	1aqd	2iam	HLA-DRB1*0101	14	GSDWRFLRGYHQYA	1.68	1.01

Cα RMSD values are calculated only for the nonamer binding core (shown in bold) for peptides with more than 9 residues in the X-ray crystal structures. X: Amino acid analogues (chemical mimics).