An effective and effecient peptide binding prediction approach for a broad set of HLA-DR molecules based on ordered weighted averaging of binding pocket profiles

Table 5 Prediction performance on the HLA-DR ligand dataset.

Allele	# ligands	OWA-PSSM	TEPITOPE	TEPITOPEpan	MultiRTA	NetMHCIIpan-2.0
DRB1*0101	53	0.827	0.833	0.834	0.833	0.835
DRB1*0102	5	0.889	0.895	0.892	0.935	0.927
DRB1*0301	88	0.667	0.673	0.671	0.652	0.789
DRB1*0401	468	0.831	0.833	0.826	0.771	0.875
DRB1*0402	36	0.882	0.885	0.880	0.768	0.667
DRB1*0403	1	0.954		0.954	1.000	0.845
DRB1*0404	42	0.779	0.775	0.797	0.711	0.765
DRB1*0405	36	0.804	0.809	0.778	0.729	0.856
DRB1*0701	47	0.698	0.697	0.696	0.720	0.744
DRB1*0801	39	0.694	0.697	0.656	0.541	0.643
DRB1*0802	1	0.930	0.916	0.923	0.532	0.978
DRB1*0803	1	0.229		0.149	0.383	0.292
DRB1*0901	6	0.750		0.659	0.842	0.957
DRB1*1001	183	0.783		0.770	0.827	0.866
DRB1*1101	35	0.828	0.835	0.831	0.838	0.896
DRB1*1104	8	0.868	0.870	0.856	0.811	0.911
DRB1*1201	11	0.801		0.828	0.847	0.863
DRB1*1301	16	0.819	0.824	0.813	0.745	0.724
DRB1*1302	19	0.743	0.742	0.735	0.720	0.561
DRB1*1401	9	0.712		0.730	0.704	0.810
DRB1*1501	22	0.720	0.718	0.717	0.663	0.671
DRB1*1502	3	0.773	0.767	0.774	0.706	0.665
DRB1*1601	2	0.621		0.630	0.918	0.849
DRB3*0101	2	0.888		0.918	0.953	0.971
DRB3*0301	5	0.907		0.783	0.939	0.948
DRB4*0101	6	0.500		0.491	0.515	0.726
DRB4*0103	2	0.941		0.753	0.745	0.827
DRB5*0101	18	0.823	0.842	0.835	0.777	0.847
Average	1164	0.774		0.756	0.754	0.797
Average I		0.799	0.801	0.795	0.732	0.786
Average II		0.735		0.697	0.789	0.814

"Average" is the average over 28 alleles. "Average I" is the average over 17 alleles predictable by TEPITOPE.
"Average II" is the average over 11 alleles not predictable by TEPITOPE. The PSSMs of TEPITOPE, TEPITOPEpan and the results of MultiRTA were obtained from their respective web servers. The prediction of NetMHCIIpan-2.0 were obtained directly from its publication.

ISSN: 1477-5956