Epitope prediction pipeline

In order to design new vaccine candidate, first we have generated nona-peptides. Nona-peptides were 9-mer sequences (9 residues continuous stretch of peptide) originated from the essential or virulent proteins selected for the study. In order to avoid redundancy, we have removed all duplicated nona-peptides.

Self-tolerance must also be considered in vaccine designing, as body's immune system rarely acts against self-epitopes. Therefore, all the nona-peptides, which are also present in human body need to be removed. To achieve this, we mapped nona-peptides on 1000 human proteome, and removed all the nona-peptides which are 100% identical.

Our subsequent objective was to select peptides, which could activate human immune system, and generate memory cells. Therefore, we have used a pipeline for predicting different kinds of immune epitopes among these nona-peptides. This pipeline predicts; (i) B-cell epitopes using LBtope (30) (ii) MHC class II binders using ProPred (31) (iii) T-cell epitopes using CTLpred (32) and (iv) vaccine adjuvant using VaxinPAD (1).

In addition to these tools, the experimentally reported epitopes present in the Immune Epitope Database (IEDB) were also mapped on the vaccine target proteins selected for this study. Figure ​Figure11 shows the complete workflow of this study.

Workflow for identification of novel vaccine candidates against pathogenic bacteria.