Table 2.

Peptide candidates selected for experimental validation

	High efficacy (HE)			Low efficacy (LE)			Alternative predictor (AP)
	Sequence	ES	ΔE	Sequence	ES	ΔE	Sequence	ES	ΔE
1	GLLALAIGL	42.3	−14.9	LEAPGLAPLSQ	0.0	−13.7	YLAEADLSYT	0.0	−9.8
	SLLGLLALA	35.7	−6.3	VAQSLENYTSKC	0.0	−1.3	SMDEANQPL	0.0	−1.7
	ALGGLVVSA	30.6	−10.8	AHFIYGYPKK	0.0	−6.2	LLQEGLKPVL	0.0	−5.3
	VLTALLAGL	21.2	−14.5	DTLPVPSGQR	0.0	−1.7	MLQDWCRWMGV	0.0	−18.4
	ALAIGLWGL	20.9	−16.8	LLLAACAPPPC	0.0	−22.2	FTLTNYTYCV	0.0	−14.3
2	LLAVLYCLL	20.6	−1.1	TDQVPFSVSVSQ	0.0	−8.3	YVAGSVILNI	0.0	−11.0
	TFLILSIAPV	19.6	−2.4	CLPRLPSPPGP	0.0	−12.5	KLNEDMTLL	0.0	−8.3
	ILAFLVLEAV	19.1	−8.0	SLEAALRPMG	0.0	−8.0	YLHSDKLKV	0.0	−13.7
	TLLVVVQPV	18.0	−19.9	DREAVAACQVGD	0.0	−0.1	RMQCESPPV	0.0	−2.9
	LLSLGCIFFPL	18.0	−9.9	YLGALCENTCL	0.0	−1.4	HMSVELLRSV	0.0	−10.4
3	LLVALIFGT*	16.9	−25.4	VRVLVARLGH	0.0	−11.5	FLQNAVYINL	0.0	−8.1
	MILGILASLV	16.7	−16.5	LAELNRIPSS	0.0	−2.5	FQNMSTFSI	0.0	−3.3
	LLGAAMVGA	15.9	−13.2	APHKEHLYKLL	0.0	−3.5	RMGNPALSV	0.0	−4.5
	FSGGILAFLV	13.6	−18.8	IAHNRGEERN	0.0	1.5	LQLEGRKLWRV	0.0	−9.9
	LLLIGCWYC	12.5	−26.1	DSESKSAVQA	0.0	−1.6	LLLLLAACA	0.0	−15.3
4	IYSMIFVILGV*	11.8	−17.5	PTSGCLGPVPRE	0.0	−9.4	YQAGCSLRL	0.0	−7.4
	VLIFPSYMTTV	11.5	−8.3	KASKGSYMEVRT	0.0	−3.8	HFLRNQPLTFAL	0.0	−9.0
	LVLMAVVLAS*	11.2	−12.4	AGTDAAGASGLQ	0.0	−14.9	RMAALRTQTL	0.0	−3.7
	GLSVIISFI	9.9	−24.5	VRCQSLGVFSG	0.0	−14.1	FRIYKRICSV	0.0	2.0
	GLLALAIGLWGL	9.2	−18.5	QGPLLGPEAVT	0.0	−12.3	KLKLCSISGL	0.0	−10.7

Each major column lists peptides of one tier, with tiers subdivided into pools of size 5. High-efficacy peptides are sorted by efficacy score.

*Peptide failed synthesis was absent from the pool during experimental tests.

ES, efficacy score (unitless); ΔE, free-energy gain of MHC-peptide complex after computational docking as calculated by RDOCK (kcal·mol^-1).