Table 2. Results of docking studies performed using HADDOCK 2.4 with selected T cell epitopes and corresponding HLA molecules.

	MHC-1					MHC-2
PDB id	5VGE	5VGE	6J1W	5VWH	3X13	2FSE	2FSE	5LAX
HLA molecule	HLA-C*07:02	HLA-C*07:02	HLA-A*30:01	HLA-B*58:01	HLA-B*08:01	HLA-DRB1*01:01	HLA-DRB1*01:01	HLA-DRB1*04:01
Epitope	PYRVVVLSF	QLTPTWRVY	HVTFFIYNK	LTWICLLQF	SPRWYFYYL	TNGVGYQPYRVVVLS	ITLKKRWQLALSKGV	LFLTWICLLQFAYAN
HADDOCK score	−30.4 ± 7.5	−8.5 ± 5.3	−65.5 ± 7.7	−10.7 ± 1.0	−29.3 ± 3.2	−38.1 ± 9.9	−23.5 ± 8.5	−78.4 ± 10.7
Cluster size	13	38	44	105	84	8	4	57
RMSD from the overall lowest-energy structure	2.4 ± 0.1	0.5 ± 0.3	0.5 ± 0.3	1.5 ± 0.2	0.6 ± 0.4	0.8 ± 0.5	0.4 ± 0.3	0.5 ± 0.3
Van der Waals energy	−46.6 ± 4.5	−58.8 ± 8.1	−64.5 ± 6.3	−52.2 ± 3.4	−62.4 ± 4.9	−65.7 ± 4.1	−52.2 ± 4.6	−74.9 ± 7.2
Electrostatic energy	−199.1 ± 10.1	−72.7 ± 27.1	−269.7 ± 30.4	−41.7 ± 9.2	−158.1 ± 11.5	−81.1 ± 24.4	−157.7 ± 51.4	−48.0 ± 6.7
Desolvation energy	−29.7 ± 0.8	−20.8 ± 1.3	−44.8 ± 3.1	−37.6 ± 2.7	−45.8 ± 3.3	−19.3 ± 1.1	−14.9 ± 2.2	−60.4 ± 2.1
Restraints violation energy	856.7 ± 73.0	856.5 ± 33.6	977.1 ± 59.8	875.0 ± 34.7	1105.8 ± 27.7	632.2 ± 117.2	752.0 ± 91.9	664.6 ± 44.5
Buried Surface Area	1803.4 ± 49.8	1575.6 ± 86.2	1840.6 ± 27.6	1471.4 ± 47.3	1612.3 ± 51.2	1681.7 ± 49.6	1722.6 ± 47.8	1985.6 ± 17.1
Z-Score	−1.2	−1.3	−1.8	−1.4	−2.1	−2.2	−1.4	−1.6