Insight into SNPs and epitopes of E protein of newly emerged genotype-I isolates of JEV from Midnapur, West Bengal, India

Table 6 Energetics of docking complex formed between epitopes and PBG of MHCs along with their conservation, accessibility and conformational stability values

IEDB Server Analyses				Shannon Variability	NACCESS Analysis	Peptide Analysis	Docking Analyses of MHCs-Peptides (Energy in Kcal Mol⁻¹)
	SL. NO.	Amino acid Position	Peptide	Average Shannon Entropy	Average side-chain Accessibility	CGE	GE	VDW^a	ACE	HB
MHC-I	1	59	YYYHASVTD	0.02	23.5	−4.70	−42.89	−16.11	−5.89	−4.74
	2	95	GFTDRGWGK	0.03	50.4	−6.61	−28.87	−21.69	−4.29	−2.42
	3	382	YIVVGRKDK	0.01	32.0	−5.52	−29.36	−11.13	−4.13	−1.95
	4	394	HHRHKAGST	0.03	64.3	−5.84	−39.03	−14.41	−2.02	−7.97
MHC-II	1	55	EVRSYYYHASVTDIS	0.04	24.7	−16.96	−48.65	−15.18	−9.98	−2.92
	2	95	GFTDRGWGKGCGLFG	0.02	57.9	−17.23	−46.57	−14.25	−5.75	−4.75
	3	380	DSYIVVGRKDKQINH	0.04	34.9	−16.07	−53.97	−22.96	−1.11	−5.02
	4	383	IVVGRKDKQINHHRH	0.00	36.8	−15.34	−52.90	−13.06	−3.63	−2.61

^aVDW is the net stabilization due to Van der Waals interactions i.e. (attractive VDW – repulsive VDW); GE global stabilization energy, ACE atomic contact energy, HB hydrogen bond, CGE coarse-grained free-energy of peptide-structure used for docking [49]

ISSN: 1471-2172