MHC2MIL: a novel multiple instance learning based method for MHC-II peptide binding prediction by considering peptide flanking region and residue positions

Table 2 Performance of MHC2MIL(fl) compared to MHCMIR(9) and MHCMIR(11). For each allele, the largest value is displayed in boldface.

allele	MHCMIR(9)	MHCMIR(11)	MHC2MIL(fl)
HLA-DPA1_01-DPB1_0401	0.772	0.780	0.778
HLA-DPA1_0103-DPB1_0201	0.782	0.792	0.790
HLA-DPA1_0201-DPB1_0101	0.810	0.811	0.817
HLA-DPA1_0201-DPB1_0501	0.784	0.790	0.791
HLA-DPA1_0301-DPB1_0402	0.820	0.832	0.832
HLA-DPB1_0301-DPB1_0401	0.785	0.782	0.791
HLA-DQA1_0101-DQB1_0501	0.763	0.761	0.768
HLA-DQA1_0102-DQB1_0602	0.751	0.760	0.763
HLA-DQA1_0301-DQB1_0302	0.666	0.665	0.672
HLA-DQA1_0401-DQB1_0402	0.732	0.721	0.737
HLA-DQA1_0501-DQB1_0201	0.772	0.758	0.779
HLA-DQA1_0501-DQB1_0301	0.804	0.800	0.809
HLA-DRB1_0101	0.770	0.789	0.786
HLA-DRB1_0301	0.793	0.805	0.808
HLA-DRB1_0401	0.738	0.735	0.741
HLA-DRB1_0404	0.793	0.773	0.791
HLA-DRB1_0405	0.790	0.784	0.792
HLA-DRB1_0701	0.809	0.819	0.819
HLA-DRB1_0802	0.700	0.717	0.712
HLA-DRB1_0901	0.730	0.723	0.733
HLA-DRB1_1101	0.831	0.825	0.834
HLA-DRB1_1302	0.736	0.741	0.745
HLA-DRB1_1501	0.752	0.767	0.765
HLA-DRB3_0101	0.749	0.740	0.756
HLA-DRB4_0101	0.787	0.776	0.787
HLA-DRB5_0101	0.796	0.792	0.803
average AUC	0.770	0.771	0.777

ISSN: 1471-2164