Design of epitope-based vaccines from tRNA peptides. The Vaccine Data Used And Download Paths to Intermediate Results are available. We initially obtained all available sequences of tRNA nucleotides from GtRNAdb from various species. It was then translated from the EMBOSSTranseq tool into equivalent peptide sequences tREP’s. These tREPs were subsequently screened for complete structural peptide selection via VaxiJen v2.0 to predict antigenic peptides. Depending on T-cell epitope prediction, these antigenic peptides are further screened based on major histocompatibility complex (MHC) class I binding, proteasomal C terminal cleavage, and TAP transport efficiency using NetCTL1.2 Server. The promising epitopes were then selected, based on cell penetration (CellPPD), toxicity (ToxinPred), antigenicity (VaxiJen v2.0), allergenicity (AllerTop v.2.0), conservancy (ECA IEDB Suite), and higher immunogenicity (C1I IEDB Suite) filtration. These epitopes should then be identified by (MHC) I alleles which are present in the endoplasmic reticulum, so that it can bind to them, and can be brought to the surface of the cell, where a T-cell or a B-cell can identify to produce an antibody. In order to bind these epitopes with alleles, the 3D structures of epitopes were generated and the corresponding allele was retrieved from RCSB to perform docking. The stability and conformational changes of these two bindings along with their dynamic interactions are then analyzed, through molecular dynamics.
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