Table 2.

Comparative performance of B cell epitope prediction methods.

Negative dataset	Method/tool	% SE	% SP	% ACC	MCC
IRPEP	BLAST	50.50	99.20	74.85	0.57
	BepiPred	37.60	65.01	51.35	0.03
	LBtope	42.21	76.34	59.32	0.20
	IBCE-EL	77.80	14.91	46.26	− 0.09
INB	BLAST	50.50	88.47	69.48	0.42
	BepiPred	37.60	66.60	52.14	0.04
	LBtope	42.41	77.73	60.02	0.20
	IBCE-EL	77.80	82.11	79.96	0.60

Table reports the sensitivity (% SE), specificity (% SP), accuracy (% ACC) and Matthew’s correlation coefficient (MMC) of the BLAST-based method, BepiPred, LBtope and IBCE-EL discriminating B cell epitopes in the BECIP dataset from non-B cell epitopes in two different datasets (IRPEP and INB). B cell epitope predictions with LBtope and IBCE-EL were carried out at the relevant web sites and BepiPred predictions were carried out using the standalone version of BepiPred (details in “Methods”).