Data on the cytotoxic T lymphocyte epitopes identified from the SARS-CoV-2 isolated in India

This fileset consists of the following datasets:

18670_NetCTLpan.xls in
xls file format

epitope_immunogenicity_score.txt
in .txt file format

NetCTLpan_out_sorted.txt
in .txt file format

The zipped folder BatchPeptideMatch-202003311256376185117084.zip
contains the following datasets:

log.txt in .txt
file format

perPeptideMatchDetails.txt
in .txt file format

139 .txt files
contained within the folder “PerPeptideMatchResults”

The 3 zipped folders
HPEPDOCK_results_3kps.tar.gz, HPEPDOCK_results_6at5.tar.gz
and HPEPDOCK_results_6o9c.tar.gz,
each contain 101 data files in .pdb file format.

Dataset 18670_NetCTLpan.xls
contains data on the cytotoxic T lymphocyte epitopes identified from the SARS-CoV-2
isolated in India as predicted by NetCTLpan.

Dataset epitope_immunogenicity_score.txt
contains the immunogenicity scores of all the predicted epitopes, after
these were subjected to the Immune Epitope Database (IEDB) immunogenicity tool.
Dataset NetCTLpan_out_sorted.txt
contains the NetCTLpan predictions for the HLA-A*03:01 allele.

Datasets log.txt and the 139 .txt files
contained within the folder “PerPeptideMatchResults”,
contain data from the peptide matching step, that was performed on sequence
dataset ‘UniProtKB release 2020_01 plus isoforms | SwissProt | Isoform’ with
target organism set as ‘Homo sapiens [9606]’.

.pdb files
contained in the three zipped folders HPEPDOCK_results_3kps.tar.gz, HPEPDOCK_results_6at5.tar.gz and HPEPDOCK_results_6o9c.tar.gz: To
further confirm the candidacy of the foreign epitopes as a vaccine, the top
three foreign epitopes based on immunogenicity scores were subjected to
molecular docking studies to confirm their interactions with the specified HLA
at the peptide-binding groove. The molecular docking of the peptide epitope
with the HLA structure was performed using HPEPDOCK Server. Each of the zipped
folders therefore contains the results of the molecular docking studies using HPEPDOCK
Server for the top three vaccine candidates (3kps, 6at5 and 6o9c).

Study aims and methodology: This study
aimed to identify cytotoxic T cell (CTL) epitopes of SARS-CoV-2 Indian isolate
for designing potential vaccine candidates which are effective on Indian population
using an in-silico approach. The
authors predicted the CTL epitopes for all those human leukocyte antigen supertypes
(HLA) which have high allelic frequently in Indian population. Additionally,
they further studied the immunogenicity, foreignness, and interactions between
the epitopes and the HLA molecules by the means of molecular docking studies.

The amino acid sequence of the
complete genome of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
isolate of India (MT050493.1) with 9950 AA was retrieved from NCBI.

NetCTLpan version 1.1 was used to predict the CTL
epitopes across the proteins coded by the SARS-CoV-2 Indian isolate.

All the predicted epitopes were subjected to the Immune
Epitope Database (IEDB) immunogenicity tool to predict their immunogenicity
score.

To filter out the vaccine candidates which are foreign
to the human body, all the epitopes that showed positive immunogenicity, were
subjected to Multiple Peptide Match tool against human reference proteome.

To further confirm the candidacy of the foreign
epitopes as a vaccine, the top three foreign epitopes based on immunogenicity
scores were subjected to molecular docking studies to confirm their
interactions with the specified HLA at the peptide-binding groove. The
molecular docking of the peptide epitope with the HLA structure was performed using
the HPEPDOCK Server.

For more details on the methodology, please read the published
article.