Immunoinformatics and Molecular Docking Studies Predicted Potential Multiepitope-Based Peptide Vaccine and Novel Compounds against Novel SARS-CoV-2 through Virtual Screening

Table 5

Selected epitopes for MEV along with their antigenicity, binding affinities, and other properties.

Sr. No.	Protein	Epitopes	Antigenicity	Binding score (kcal/Mol) with HLA-B7	Predicted MHC binding affinity	Rescale binding affinity	C-terminal cleavage affinity	TAP transport efficiency	Position
MHC class I
1	Nsp1	HVGEIPVAY	0.81	-11.76	1.193	4.366	0.229	1.702	37-45
2	Nsp1	LSEARQHLK	0.16	-11.55	0.325	3.659	0.852	2.957	60-68
3	Replicase	GSVGFNIDY	1.52	-14.25	1.212	0.311	0.955	0.857	12-21
4	Replicase	LLEDEFTPF	2.37	-10.22	1.651	2.146	0.972	3.998	31-39
5	Envelope	LVKPSFYVY	0.63	-10.36	1.297	3.905	0.942	2.706	9-17
6	Membrane	LVGLMWLSY	0.54	-10.87	0.176	2.718	0.755	0.723	54-62
7	Membrane	AGDSGFAAY	0.52	-15.00	0.158	2.649	0.806	1.676	93-101
8	Nucleocapsid	LSPRWYFYY	0.87	-14.78	0.113	2.480	0.973	2.518	99-107
9	Nucleocapsid	SSPDDQIGY	0.65	-13.57	0.693	0.369	0.621	2.602	154-162
10	Spikes	WTAGAAAYY	0.35	-12.22	0.625	1.659	0.892	2.937	27-35
11	Spikes	CNDPFLGVY	1.32	-12.63	0.812	6.211	0.365	2.857	59-67
12	Spikes	ITDAVDCAL	1.52	-15.21	0.713	3.369	0.629	2.700	71-79
13	Spikes	STQDLFLPF	0.57	-11.36	0.631	0.651	0.880	2.857	88-96
14	Spikes	QLTPTWRVY	2.0	-10.28	0.302	2.611	0.915	2.352	112-120
15	Spikes	VLPFNDGVY	1.70	-14.27	0.005	3.106	0.025	2.908	137-145
16	Spikes	YQDVNCTEV	0.08	-14.26	0.117	2.835	0.932	2.716	199-207
MHC class II
17	Nsp1	DLGDELGTDPYEDFQ	0.12	-11.32	0.693	2.366	0.663	2.976	69-83
18	Replicase	TLNGLWLDDVVYCPR	0.77	-12.88	0.723	0.659	0.872	2.126	101-115
19	Envelope	VLLFLAFVVFLLVTL	2.52	-11.01	1.556	3.311	0.365	2.357	99-113
20	Membrane	LACFVLAAVYRINWI	1.37	-13.73	1.327	2.146	0.985	2.256	127-141
21	Membrane	CLLQFAYANRNRFLY	0.33	-14.58	0.786	2.805	0.900	2.799	196-210
22	Membrane	AVYRINWITGGIAIA	0.55	-10.27	0.456	1.718	0.002	2.159	222-236
23	Nucleocapsid	QIGYYRRATRRIRGG	0.83	-10.66	0.551	4.648	0.116	2.015	13-27
24	Nucleocapsid	GTWLTYTGAIKLDDK	1.54	-13.22	1.007	3.487	0.963	2.367	47-61
25	Nucleocapsid	ATKAYNVTQAFGRRG	1.12	-13.37	1.697	0.369	0.129	2.449	68-82
26	Nucleocapsid	GDAALALLLLDRLNQ	2.54	-15.24	0.273	0.559	0.652	2.441	171-185
27	Spikes	QSLLIVNNATNVVIK	1.02	-10.25	0.123	2.311	0.756	2.221	9-23
28	Spikes	INITRFQTLLALHRS	2.38	-12.16	0.357	3.116	0.925	2.118	166-180