Table 3.

Comparison between modeled peptides and relevant crystal structures after docking onto a single template

Class	Allele	PDB	Length	Template	RMSD (Å)	Sequence
I	HLA-A*0201	1DUZ	9	1I4F	0.69	LLFGYPVYV
I	HLA-A*0201	1HHG	9	1I4F	0.58	TLTSCNTSV
I	HLA-A*0201	1HHJ	9	1I4F	0.73	ILKEPVHGV
I	HLA-A*0201	1HHH	10	1I4F	1.48	FLPSDFFPSV
I	HLA-A*0201	1I1Y	9	1I4F	0.77	YLKEPVHGV
I	HLA-A*0201	1I7R	9	1I4F	0.60	FAPGFFPYL
I	HLA-A*0201	1I7U	9	1I4F	0.70	ALWGFVPVL
I	HLA-A*0201	1JF1	10	1I4F	1.20	ELAGIGILTV
I	HLA-A*0201	1JHT	9	1I4F	1.09	ALGIGILTV
I	HLA-A*0201	1OGA	9	1I4F	0.38	GILGFVFTL
I	HLA-A*0201	1QRN	9	1I4F	0.81	LLFGYAVYV
I	HLA-A*0201	1QSE	9	1I4F	0.52	LLFGYPRYV
I	HLA-A*0201	1QSF	9	1I4F	0.57	LLFGYPVAV
II	HLA-DR2	1BX2	10	1FV1	1.22	VVHFFKNIVT
II	HLA-DR4	2SEB	10	1J8H	0.42	KYVKQNTLKL

RMSD values calculated for the ligand interface Cα atoms of the lowest energy solution superimposed onto the experimental PDB structure are listed.