Table 3.

Metrics for estimating the quality of neutralising epitope prediction.

protein	baseline	TP	FP	TN	FN	sensitivity	specificity	accuracy	precision	MCC
gp110	5.72%	26	141	667	23	0.53	0.83	0.81	0.16	0.21
gp350 (no repeat)	8.05%	47	224	615	26	0.64	0.73	0.73	0.17	0.22
gp350 (single repeat)	8.05%	59	224	615	14	0.81	0.73	0.74	0.21	0.32
gp350	12.35%	95	224	576	17	0.85	0.72	0.74	0.3	0.39

Table 3 provides TP (True Positives), FP (False Positives), TN (True Negatives), FN (False Negatives), MCC (Matthews correlation coefficient) for selected sequences. The baseline value corresponds to the percentage of residues belonging to neutralizing epitopes. For gp350 tree entries have been added, depending whether a single copy of ‘VTTPTPNATSPT’ is interpreted as False Negatives (FN), namely i) no repeats are considered as predicted, ii) a single repeat is accepted as predicted, or iii) all four copies are accepted as predicted (default).