Structure-aware deep model for MHC-II peptide binding affinity prediction

BMC Genomics

Table 1 Performance (AUC) of using different positional encoding conditions and DeepMHCII on ID2017. ’O’ denotes using peptide-PE only, and ’T’ denotes using peptide-PE and MHC-II-PE together

Allele	DeepMHCII	Calibrated PE				Direct PE
Allele	DeepMHCII	Pre (O)	Pre (T)	Post (O)	Post (T)	Pre (O)	Pre (T)	Post (O)	Post (T)
DRB1*0101	0.882	0.868	0.873	0.885	0.871	0.883	0.883	0.875	0.877
DRB1*0301	0.629	0.602	0.676	0.622	0.632	0.628	0.620	0.629	0.610
DRB1*0401	0.863	0.813	0.790	0.854	0.814	0.807	0.778	0.810	0.816
DRB1*0701	0.814	0.792	0.845	0.802	0.823	0.812	0.821	0.825	0.821
DRB1*0901	0.889	0.875	0.844	0.893	0.859	0.856	0.844	0.841	0.842
DRB1*1101	0.657	0.642	0.649	0.658	0.648	0.652	0.641	0.628	0.633
DRB1*1202	0.788	0.758	0.811	0.763	0.725	0.788	0.733	0.716	0.735
DRB1*1301	0.615	0.566	0.736	0.636	0.660	0.517	0.651	0.643	0.572
DRB1*1501	0.799	0.798	0.821	0.807	0.823	0.810	0.798	0.817	0.806
DRB1*1502	0.764	0.752	0.728	0.734	0.700	0.726	0.720	0.679	0.687
Average	0.770	0.747	0.777	0.765	0.755	0.748	0.749	0.746	0.740

ISSN: 1471-2164