USMPep: universal sequence models for major histocompatibility complex binding affinity prediction

BMC Bioinformatics

Table 2 Details of training and test datasets

Dataset	Usage	Total size	Share of binders	# alleles	Median size	Share of quant. meas.	Sequence length
MHC class I
BD2009	train	117326	0.25	53	1971	0.58	8–11
Blind	test	27680	0.33	53	470	0.58	8–11
MHCFlurry18	train	120720	0.25	32	3659	0.68	8–15
IEDB16_I	test	2827	0.54	32	73	1.0	9
MHCFlurry18	train	68117	0.26	7	6884	0.64	8–15
HPV	test	743	0.34	7	125	0.37	8–11
MHC class II
Wang10	train	23203	0.37	24	999	1.0	15–37
IEDB16_II	test	15691	0.33	24	641	1.0	15

The threshold for MHC class I binders is 500nM, except for the HPV dataset, where the threshold is 100 000nM. For MHC class II binders, the threshold is 1000nM

ISSN: 1471-2105