Peptide binding predictions for HLA DR, DP and DQ molecules

BMC Bioinformatics

Table 3 Comparison of ARB, SMM-align and PROPRED's performance on current and old dataset.

Allelic variant	ARB		SMM-align		PROPRED
	Current ¹	Old ²	current ¹	old ²	current ¹	old ²
HLA-DPA10103-DPB10201	0.823		0.921
HLA-DPA101-DPB10401	0.847		0.930
HLA-DPA10201-DPB10101	0.824		0.909
HLA-DPA10201-DPB10501	0.859		0.923
HLA-DPA10301-DPB10402	0.821		0.932
HLA-DQA10101-DQB10501	0.871		0.930
HLA-DQA10102-DQB10602	0.777		0.838
HLA-DQA10301-DQB10302	0.748		0.807
HLA-DQA10401-DQB10402	0.845		0.896
HLA-DQA10501-DQB10201	0.855		0.901
HLA-DQA10501-DQB10301	0.844		0.910
HLA-DRB1*0101	0.770	0.764	0.798	0.769	0.720	0.738
HLA-DRB1*0301	0.753	0.660	0.852	0.693	0.699	0.652
HLA-DRB1*0401	0.731	0.667	0.781	0.684	0.737	0.686
HLA-DRB1*0404	0.707	0.724	0.816	0.753	0.769	0.789
HLA-DRB1*0405	0.771	0.669	0.822	0.694	0.767	0.750
HLA-DRB1*0701	0.767	0.692	0.834	0.776	0.773	0.776
HLA-DRB1*0802	0.702	0.737	0.741	0.750	0.647	0.768
HLA-DRB1*0901	0.747	0.622	0.765	0.660
HLA-DRB1*1101	0.800	0.731	0.864	0.808	0.804	0.796
HLA-DRB1*1302	0.727	0.787	0.797	0.695	0.600	0.584
HLA-DRB1*1501	0.763	0.700	0.796	0.738	0.743	0.715
HLA-DRB3*0101	0.709	0.590	0.819	0.677
HLA-DRB4*0101	0.785	0.741	0.816	0.713
HLA-DRB5*0101	0.760	0.703	0.832	0.751	0.728	0.790
H-2-IAb	0.800	0.803	0.855	0.746
Average	0.784	0.706	0.849	0.727	0.726	0.731
Min	0.702	0.590	0.741	0.660	0.600	0.584
Max	0.871	0.803	0.932	0.808	0.804	0.796

Best prediction performance for each allelic variant was highlighted in bold.
1. The current AUC values for ARB and SMM-align were derived by cross-validation. The current AUC values for PROPRED were derived by predicting affinities for the new dataset.
2. The old AUC values were taken from previous evaluation [30].

ISSN: 1471-2105