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

Immunome Research

Table 5 Docking promiscuous peptides onto variant templates: comparison of pDOCK with our previous method.

MHC class	Peptide PDB Allele	Peptide PDB	MHC Template Structure	Template Allele	Peptide Length	Peptide Sequence	Cα RMSD compared to template peptides (Å)
							Previous method	pDOCK
I	HLA-B*3501	1zhk^#	1zhl^#	HLA-B*3508	13	LPEPLPQGQLTAY	0.62	0.44
I	HLA-B*3501	1zsd^#	2ak4	HLA-B*3508	11	EPLPQGQLTAY	1.15	0.79
I	H2-Kb	2vaa^#	1ce6	H2-Db	9	FAPGNYPAL	0.73	0.21
II	HLA-DRB1*1501	1bx2^#	1fv1	HLA-DRB5*0101	14	ENPVVHFFKNIVTP	1.01	0.22

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. ^# The structures are not listed in Additional file – Table S1 due to redundancy in MPID-T2.