Peptide binding predictions for HLA DR, DP and DQ molecules

Wang, Peng; Sidney, John; Kim, Yohan; Sette, Alessandro; Lund, Ole; Nielsen, Morten; Peters, Bjoern

doi:10.1186/1471-2105-11-568

BMC Bioinformatics

Table 4 Cross validation prediction performances of all methods on complete and similarity reduced datasets measured with AUC.

From: Peptide binding predictions for HLA DR, DP and DQ molecules

Allelic variant	ARB		SMM-align		PROPRED		combinatorial library		NN-align		Consensus		Consensus-best3²
	ALL	SR ¹	ALL	SR ¹	ALL	SR ¹	ALL	SR ¹	ALL	SR ¹	ALL	SR ¹	ALL	SR ¹
HLA-DPA10103-DPB10201	0.823	0.745	0.921	0.767			0.840	0.724	0.943	0.793	0.932	0.809	0.935	0.796
HLA-DPA101-DPB10401	0.847	0.746	0.930	0.767			0.833	0.704	0.947	0.802	0.938	0.803	0.941	0.794
HLA-DPA10201-DPB10101	0.824	0.743	0.909	0.786			0.849	0.723	0.944	0.818	0.927	0.818	0.932	0.819
HLA-DPA10201-DPB10501	0.859	0.709	0.923	0.728			0.867	0.729	0.956	0.787	0.942	0.781	0.946	0.782
HLA-DPA10301-DPB10402	0.821	0.771	0.932	0.818			0.864	0.756	0.949	0.828	0.938	0.841	0.941	0.830
HLA-DQA10101-DQB10501	0.871	0.741	0.930	0.783			0.809	0.728	0.945	0.805	0.933	0.809	0.942	0.811
HLA-DQA10102-DQB10602	0.777	0.708	0.838	0.734			0.765	0.752	0.880	0.762	0.851	0.778	0.859	0.779
HLA-DQA10301-DQB10302	0.748	0.637	0.807	0.663			0.698	0.616	0.851	0.693	0.823	0.690	0.837	0.692
HLA-DQA10401-DQB10402	0.845	0.643	0.896	0.761			0.681	0.637	0.922	0.742	0.908	0.749	0.916	0.762
HLA-DQA10501-DQB10201	0.855	0.700	0.901	0.736			0.586	0.620	0.932	0.777	0.917	0.774	0.923	0.779
HLA-DQA10501-DQB10301	0.844	0.756	0.910	0.801			0.802	0.745	0.927	0.811	0.917	0.814	0.919	0.816
HLA-DRB1*0101	0.770	0.710	0.798	0.756	0.720	0.692	0.739	0.697	0.843	0.763	0.810	0.759	0.820	0.769
HLA-DRB1*0301	0.753	0.728	0.852	0.808	0.699	0.669			0.887	0.829	0.862	0.823	0.873	0.835
HLA-DRB1*0401	0.731	0.668	0.781	0.721	0.737	0.711			0.813	0.734	0.799	0.735	0.804	0.738
HLA-DRB1*0404	0.707	0.681	0.816	0.789	0.769	0.753			0.823	0.803	0.826	0.800	0.831	0.809
HLA-DRB1*0405	0.771	0.716	0.822	0.767	0.767	0.742			0.870	0.794	0.847	0.797	0.851	0.797
HLA-DRB1*0701	0.767	0.736	0.834	0.796	0.773	0.750	0.762	0.729	0.869	0.811	0.851	0.806	0.858	0.808
HLA-DRB1*0802	0.702	0.649	0.741	0.689	0.647	0.641			0.796	0.698	0.772	0.708	0.778	0.710
HLA-DRB1*0901	0.747	0.654	0.765	0.696			0.572	0.553	0.810	0.713	0.801	0.716	0.796	0.716
HLA-DRB1*1101	0.800	0.777	0.864	0.829	0.804	0.779			0.900	0.847	0.880	0.850	0.885	0.854
HLA-DRB1*1302	0.727	0.667	0.797	0.754	0.600	0.577			0.814	0.732	0.796	0.742	0.811	0.757
HLA-DRB1*1501	0.763	0.696	0.796	0.741	0.743	0.703			0.852	0.756	0.820	0.756	0.827	0.758
HLA-DRB3*0101	0.709	0.678	0.819	0.780			0.655	0.655	0.856	0.798	0.834	0.787	0.844	0.799
HLA-DRB4*0101	0.785	0.747	0.816	0.762			0.697	0.691	0.870	0.789	0.844	0.791	0.846	0.784
HLA-DRB5*0101	0.760	0.697	0.832	0.776	0.728	0.711			0.886	0.795	0.848	0.786	0.851	0.798
H-2-IAb	0.800	0.775	0.855	0.830					0.858	0.847	0.853	0.846	0.866	0.847
Average	0.785	0.711	0.850	0.763	0.726	0.703	0.751	0.691	0.882	0.782	0.864	0.783	0.871	0.786
Min	0.702	0.637	0.741	0.663	0.600	0.577	0.572	0.553	0.796	0.693	0.772	0.690	0.778	0.692
Max	0.871	0.777	0.932	0.830	0.804	0.779	0.867	0.756	0.956	0.847	0.942	0.850	0.946	0.854

1. SR¹stands for similarity reduced.
2. The Consensus-best3 method is based on NN-align, SMM-align and combinatorial peptide library. PROPRED was used for allelic variants when combinatorial peptide library was not available
Best prediction performance for each allelic variant was highlighted. The best performing method for "ALL" dataset was highlighted with underline while the best performing method for "SR" dataset was highlighted in bold.

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ISSN: 1471-2105

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