Table 1.

MHC-II binding affinities of all overlapping 15-mers in the surfome of Staphylococcus aureus COL NC_002951.

MHC-II Supertype	Ave ln(ic50)	Std Dev ln(ic50)	10%-tile ln(ic50)	Ave IC50 (nM)	Ave-SD ic50 (nM)	10%-tile ic50 (nM)	Ave-2SD ic50 (nM)
DRB1_0101	4.48	3.11	0.54	88.27	3.95	1.72	0.18
DRB1_0301	6.29	1.93	3.81	540.59	78.15	45.28	11.30
DRB1_0401	5.31	2.59	1.95	202.23	15.12	7.04	1.13
DRB1_0404	5.23	2.76	1.63	187.57	11.84	5.12	0.75
DRB1_0405	4.38	1.90	1.92	79.92	11.96	6.81	1.79
DRB1_0701	4.29	2.84	0.62	73.33	4.27	1.85	0.25
DRB1_0802	7.05	2.00	4.48	1151.07	155.45	88.42	20.99
DRB1_0901	5.85	2.48	2.64	346.90	29.03	13.99	2.43
DRB1_1101	5.58	2.52	2.35	265.50	21.39	10.46	1.72
DRB1_1302	7.14	1.95	4.62	1257.67	178.85	101.68	25.43
DRB1_1501	5.86	2.74	2.31	351.12	22.61	10.07	1.46
DRB3_0101	8.26	1.95	5.74	3861.57	547.81	312.37	77.71
DRB4_0101	5.69	2.20	2.81	294.70	32.68	16.67	3.62
DRB5_0101	4.92	2.60	1.58	136.76	10.12	4.85	0.75
Average	5.74	2.40	2.64	631.2	80.2	44.7	10.7
Exp(Average) nM	310.5	11.0	14.1

The surface proteome consists of all proteins that have one or more predicted transmembrane helices in their structure. The statistics were derived from approximately 216,000 15-mers for 14 supertypes, or about 3.02 million binding predictions. The NN were trained and the predictions were made in the natural logarithmic domain (ln). The statistical parameters are for the entire proteome, as this would constitute the population of peptides presented binding to MHC molecules on the surface of antigen presenting cells.