BMC Bioinformatics

Table 3 A comparison of peptide binding register prediction results for the peptide-MHC complexes listed in Table 5 using RTA and seven other prediction methods

From: Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model

		Prediction Method
Class II MHC allotype	PDB entry	RTA	ARB	MHC2Pred	NN-align	ProPred	RANKPEP	SMM-align	SVRMHC
DRB1*0101	1AQD	✔	✘	✘	✔	✔	✔	✔	✔
	1DLH	✔	NA	✔	✔	✔	✔	NA	✔
	1KLG	✔	✔	✘	✔	✔	✔	✔	✘
	1KLU	✔	✔	✘	✔	✔	✔	✔	✘
	1SJE	✔	✔	✔	✔	✔	✘	✔	✔
	1T5W	✔	✔	✘	✔	✔	✔	✔	✘
	2FSE	✔	NA	✘	✔	✔	✔	NA	✘
DRB1*0301	1A6A	✔	✔	✘	✔	✔	✘	✔	NA
DRB1*0401	1J8H	✔	NA	✔	✔	✔	✔	NA	✘
	2SEB	✔	NA	✔	✘	✔	✘	NA	✘
DRB1*1501	1BX2	✔	✘	✘	✔	✔	✔	✔	✔
DRB3*0101	2Q6W	✔	NA	NA	✔	✔	NA	NA	NA
DRB5*0101	1FV1	✔	✘	✘	✔	✔	✘	✘	✔
	1H15	✔	NA	✘	✔	✔	✘	NA	✔
H2-IA^b	1LNU	✔	NA	✘	✘	NA	✔	NA	NA
	1MUJ	✔	✔	✘	✔	NA	✔	✘	NA
H2-IA^d	1IAO	✘	✔	✘	✘	NA	✘	✘	NA
	2IAD	✔	✔	✘	✘	NA	✘	✘	NA
Total correct		17/18	8/11	4/17	14/18	14/14	10/17	7/11	6/12

"✔" indicates a correct prediction and "✘" indicates an incorrect one. "NA" denotes that a prediction is not available either because the method does not have a prediction model for that MHC type or the method cannot be applied to a peptide shorter than 15 residues.

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