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

Immunome Research

Table 3 Comparison of pDOCK with published MHC–peptide modeling and flexible docking methods.

S.No	Technique	Peptide Sequence	MHC class	PDB	RMSD (Å)
					Published	Previousmethod	pDOCK
1	Grid-based Flexible docking [34]	RGYVYQGL	I	1kpu^#	0.76	0.59	0.31
2	Grid-based Flexible docking [34]	ALWGFVPVL	I	1i7u	0.23	0.32	0.29
3	Grid-based Flexible docking [34]	ELAGIGILTV	I	1jf1	0.22	1.53	0.30
4	Monte Carlo annealing [37]	LLFGYPVYV	I	1duz^#	3.01	0.33	0.33
5	Simulated annealing [38]	FLPSDFFPSV	I	1hhh	1.59	1.10	0.48
6	Simulated annealing [38]	GILGFVFTL	I	1hhi^#	0.46	0.32	0.16
7	Simulated annealing [38]	ILKEPVHGV	I	1hhj^#	0.87	0.87	0.55
8	Simulated annealing [38]	LLFGYPVYV	I	1hhk^#	0.78	0.33	0.33
9	Combinatorial buildup algorithm [39]	RGYVYQGL	I	2vaa^#	0.56	0.32	0.22
10	Combinatorial buildup algorithm [40]	LLFGYPVYV	I	1hhk^#	1.40	0.33	0.33
11	Combinatorial buildup algorithm [40]	ILKEPVHGV	I	1hhj^#	1.30	0.87	0.55
12	Combinatorial buildup algorithm [40]	GILGFVFTL	I	1hhi^#	1.60	0.32	0.16
13	Multiple copy algorithm [41]	FAPGNYPAL	I	2vab^#	2.70	0.40	0.25
14	Multiple copy algorithm [42]	GILGFVFTL	I	1hhi^#	1.40	0.32	0.16
15	GOLD/GLIDE Flexible docking [36]	XXRXMASX	II	1d6e	1.24/3.06	0.32	0.14

X: Amino acid analogues (chemical mimics). ^#These structures are not listed in Additional File 1- Table S1 due to redundancy in MPID-T2.