PREDTAP: a system for prediction of peptide binding to the human transporter associated with antigen processing

Table 7 Amino acid position of top 3% predicted TAP binders in the tumor antigen KM-HN-1 (NP_689988.1) by SVMTAP, TAPPred and PRED^TAP. The positions marked by "+" were selected by four prediction models and those marked by "*"were selected by three prediction models. The predicted TAP-binders in proximity of known T-cell epitopes are designated by ¹(196–204), ²(499–508) and ³(770–778)

SVMTAP	TAPPred (SVM)	TAPPred (Cascade SVM)	PRED^TAP (ANN)		PRED^TAP (HMM)
Position	Position	Position	Position	Score	Position	Score
660⁺	372⁺	674	195^1,+	8.15	682	7.01
372⁺	195^1,+	314	654*	8.09	506^2,+	6.98
426*	426*	639	372⁺	8.06	372⁺	6.87
195^1,+	794	249	422	7.94	683	6.83
794	330	530	565	7.41	507⁺	6.65
199	317⁺	525	317⁺	6.53	195^1,+	6.62
654*	660⁺	325	310	5.97	492	6.44
317⁺	331	206	378	5.59	310	6.41
371	652*	12	468	5.54	660⁺	6.41
110	199	479	763³	5.48	16	6.37
760	198	537	337	5.36	468	6.33
198	371	112	426*	5.33	317⁺	6.19
789	654*	93	737	5.16	395*	6.16
705	506^2,+	626	246	5.04	573	6.12
457	789	470	660⁺	4.98	223	6.12
507⁺	457	141	756	4.96	193	6.09
48	730	483	110	4.95	730	6.09
573	304	71	506^2,+	4.89	313	6.05
376	565	99	201	4.79	647	6.05
652*	395*	668	507⁺	4.76	510	6.01
395*	760	781	365	4.64	652*	6.01
780	318	57	653	4.55	15	6.01
455	764³	579	502²	4.52	814	6.01
506^2,+	63	124	492	4.44	676	5.94
324	507⁺	590	456	4.43	782	5.94