Table 3.

MHC-II binding affinity of heterozygous and homozygous pairs

	S1	S2	10%tile S1	10%tile S2	10%tile Average	10%tile min of pair
Top Ten	DRB1_0101	DRB1_0101	0.54	0.54	0.54	0.54
	DRB1_0301	DRB1_0101	3.81	0.54	2.175	0.54
	DRB1_0401	DRB1_0101	1.95	0.54	1.245	0.54
	DRB1_0404	DRB1_0101	1.63	0.54	1.085	0.54
	DRB1_0405	DRB1_0101	1.92	0.54	1.23	0.54
	DRB1_0701	DRB1_0101	0.62	0.54	0.58	0.54
	DRB1_0802	DRB1_0101	4.48	0.54	2.51	0.54
	DRB1_0901	DRB1_0101	2.64	0.54	1.59	0.54
	DRB1_1101	DRB1_0101	2.35	0.54	1.445	0.54
	DRB1_1302	DRB1_0101	4.62	0.54	2.58	0.54
Bottom Ten	DRB1_0301	DRB1_0301	3.81	3.81	3.81	3.81
	DRB1_0802	DRB1_0301	4.48	3.81	4.145	3.81
	DRB1_1302	DRB1_0301	4.62	3.81	4.215	3.81
	DRB3_0101	DRB1_0301	5.74	3.81	4.775	3.81
	DRB1_0802	DRB1_0802	4.48	4.48	4.48	4.48
	DRB1_1302	DRB1_0802	4.62	4.48	4.55	4.48
	DRB3_0101	DRB1_0802	5.74	4.48	5.11	4.48
	DRB1_1302	DRB1_1302	4.62	4.62	4.62	4.62
	DRB3_0101	DRB1_1302	5.74	4.62	5.18	4.62
	DRB3_0101	DRB3_0101	5.74	5.74	5.74	5.74
		Mean	2.92	2.37	2.64	1.88
		Std Dev	1.47	1.41	1.07	1.08

Ten percentile MHC-II binding affinity statistics for 105 different heterozygous and homozygous supertype combinations for 15-mer peptides from the surface proteome of Staphylococcus aureus COL. The results were obtained using 14 MHC-II supertypes for which training sets were available to train the NN. The surface proteome is defined as proteins that are predicted to have one or more transmembrane helices and are therefore expected to be inserted into the cell membrane. Top and bottom ten pairs are shown in this summary table; complete data set in Additional File 6.