Peptide binding predictions for HLA DR, DP and DQ molecules

BMC Bioinformatics

Table 2 Overview of MHC class II binding dataset utilized in the present study.

Allelic variant	# of binding affinities	# of binders¹	% of binders	Allele frequency²
HLA-DPA10201-DPB10101	1399	702	0.5	16.0
HLA-DPA10103-DPB10201	1404	635	0.45	17.5
HLA-DPA101-DPB10401	1337	540	0.4	36.2
HLA-DPA10301-DPB10402	1407	621	0.44	41.6
HLA-DPA10201-DPB10501	1410	528	0.37	21.7
HLA-DQA10501-DQB10201	1658	742	0.45	11.3
HLA-DQA10501-DQB10301	1689	1023	0.61	35.1
HLA-DQA10301-DQB10302	1719	670	0.39	19.0
HLA-DQA10401-DQB10402	1701	731	0.43	12.8
HLA-DQA10101-DQB10501	1739	687	0.4	14.6
HLA-DQA10102-DQB10602	1629	974	0.6	14.6
HLA-DRB1*0101	6427	4519	0.7	5.4
HLA-DRB1*0301	1715	553	0.32	13.7
HLA-DRB1*0401	1769	978	0.55	4.6
HLA-DRB1*0404	577	396	0.69	3.6
HLA-DRB1*0405	1582	806	0.51	6.2
HLA-DRB1*0701	1745	1033	0.59	13.5
HLA-DRB1*0802	1520	591	0.39	4.9
HLA-DRB1*0901	1520	815	0.54	6.2
HLA-DRB1*1101	1794	957	0.53	11.8
HLA-DRB1*1302	1580	656	0.42	7.7
HLA-DRB1*1501	1769	909	0.51	12.2
HLA-DRB3*0101	1501	426	0.28	26.1
HLA-DRB4*0101	1521	654	0.43	41.8
HLA-DRB5*0101	1769	992	0.56	16.0
H-2-IAb	660	180	0.27	-
Total	44541	22318
Min	577	180
Max	6427	4519
DP				92.6
DQ				81.6
DRB1				71.0
DRB3/4/5				70.9
Total				99.9

1. Binder defined as IC50 <1000 nM.
2. Average haplotype and phenotype frequencies for individual alleles are based on data available at dbMHC. dbMHC data considers prevalence in Europe, North Africa, North-East Asia, the South Pacific (Australia and Oceania), Hispanic North and South America, American Indian, South-East Asia, South-West Asia, and Sub-Saharan Africa populations. DP, DRB1 and DRB3/4/5 frequencies consider only the beta chain frequency, given that the DRA chain is largely monomorphic, and that differences in DPA are not hypothesized to significantly influence binding. Frequency data are not available for DRB3/4/5 alleles. However, because of linkage with DRB1 alleles, coverage for these specificities may be assumed as follows: DRB3 with DR3, DR11, DR12, DR13 and DR14; DRB4 with DR4, DR7 and DR9; DRB5 with DR15 and DR16. Specific allele frequencies at each B3/B4/B5 locus is based on published associations with various DRB1 alleles, and assumes only limited variation at the indicated locus.

ISSN: 1471-2105