Table 3.

Results of MHC-PPM in MHC class II predictions in Wang2010 dataset [23].

Allele	# Peptides		ARB		SMM-align		NN-align		MHC-PPM
	ALL	SR	ALL	SR	ALL	SR	ALL	SR	ALL	SR
HLA-DPA1*0103-DPB1*0201	1404	603	0.823	0.745	0.921	0.767	0.943	0.793	0.931	0.772
HLA-DPA1*01-DPB1*0401	1337	540	0.847	0.746	0.930	0.767	0.947	0.802	0.935	0.751
HLA-DPA1*0201-DPB1*0101	1399	604	0.824	0.743	0.909	0.786	0.944	0.818	0.938	0.806
HLA-DPA1*0201-DPB1*0501	1410	586	0.859	0.709	0.923	0.728	0.956	0.787	0.948	0.773
HLA-DPA1*0301-DPB1*0402	1407	602	0.821	0.771	0.932	0.818	0.949	0.828	0.935	0.815
HLA-DQA1*0101-DQB1*0501	1739	584	0.871	0.741	0.930	0.783	0.945	0.805	0.949	0.754
HLA-DQA1*0102-DQB1*0602	1629	593	0.777	0.708	0.838	0.734	0.880	0.762	0.842	0.730
HLA-DQA1*0301-DQB1*0302	1719	596	0.748	0.637	0.807	0.663	0.851	0.693	0.845	0.709
HLA-DQA1*0401-DQB1*0402	1701	585	0.845	0.643	0.896	0.761	0.922	0.742	0.920	0.778
HLA-DQA1*0501-DQB1*0201	1658	589	0.855	0.700	0.901	0.736	0.932	0.777	0.919	0.766
HLA-DQA1*0501-DQB1*0301	1689	602	0.844	0.756	0.910	0.801	0.927	0.811	0.915	0.771
HLA-DRB1*0101	6427	3504	0.770	0.710	0.798	0.756	0.843	0.763	0.821	0.758
HLA-DRB1*0301	1715	1136	0.753	0.728	0.852	0.808	0.887	0.829	0.828	0.747
HLA-DRB1*0401	1769	1221	0.731	0.668	0.781	0.721	0.813	0.734	0.763	0.711
HLA-DRB1*0404	577	474	0.707	0.681	0.816	0.789	0.823	0.803	0.885	0.717
HLA-DRB1*0405	1582	1049	0.771	0.716	0.822	0.767	0.870	0.794	0.831	0.734
HLA-DRB1*0701	1745	1175	0.767	0.736	0.834	0.796	0.869	0.811	0.846	0.804
HLA-DRB1*0802	1520	1017	0.702	0.649	0.741	0.689	0.796	0.698	0.752	0.687
HLA-DRB1*0901	1520	1042	0.747	0.654	0.765	0.696	0.810	0.713	0.762	0.671
HLA-DRB1*1101	1794	1204	0.800	0.777	0.864	0.829	0.900	0.847	0.858	0.811
HLA-DRB1*1302	1580	1070	0.727	0.667	0.797	0.754	0.814	0.732	0.768	0.717
HLA-DRB1*1501	1769	1171	0.763	0.696	0.796	0.741	0.852	0.756	0.813	0.745
HLA-DRB3*0101	1501	987	0.709	0.678	0.819	0.780	0.856	0.798	0.782	0.718
HLA-DRB4*0101	1521	1011	0.785	0.747	0.816	0.762	0.870	0.789	0.860	0.772
HLA-DRB5*0101	1769	1198	0.760	0.697	0.832	0.776	0.886	0.795	0.843	0.812
H-2-Iab	660	546	0.800	0.775	0.855	0.830	0.858	0.847	0.824	0.807
Average			0.785	0.711	0.849	0.763	0.882	0.782	0.858	0.755
WeightedAverage			0.784	0.709	0.843	0.762	0.879	0.778	0.853	0.754

Each method contains results from all of the peptides (ALL) and the similarity reduced data (SR). The best-performing method for each allele in ALL dataset is marked by bold and the best performing method in SR dataset is underlined.