Table 1 Details of the computational tools used for the prediction of antigens, epitopes and their population coverage analysis
S.No. | Database/tool name | Description | URL | Threshold criteria |
|---|---|---|---|---|
1 | SignalP4.0 | Presence and location of signal peptide cleavage sites | Default | |
2 | PredGPI | Prediction system for GPI-anchored proteins | Default | |
3 | MAAP | Prediction of Malarial adhesins and adhesins-like proteins. | ≥ 0 | |
4 | TMHMM2.0 | Transmembrane helices in the integral membrane proteins | ≤ 1 | |
5 | VaxiJen2.0 | Prediction of protective antigens | ≥ 0.5 | |
6 | ExPASy-ProtParam | Calculation of physicochemical parameters | Default | |
7 | MAFFT7.0 | Multiple sequence alignment | Default | |
8 | INNOVAGEN | Prediction of water solubility of proteins | Default | |
9 | IEDB-MHC class I-Consensus | Prediction of MHC class I binding epitopes | IC50 ≤ 500 nM | |
10 | IEDB-MHC class II-Consensus | Prediction of MHC class II binding epitopes | ≤ 3 percentile rank | |
11 | IEDB-Population Coverage | Population coverage analysis of selected epitopes | Default | |
12 | CTLPred | Prediction of cytotoxic T cell epitopes | Default | |
13 | IL-10Pred | Prediction of IL-10 inducer epitopes | Default | |
14 | TAPPred | Prediction of TAP binding affinity of epitopes | Default | |
15 | IFNepitope | Prediction of IFN-γ inducer epitopes | Default | |
16 | PEP-FOLD 3 | Peptide and miniprotein structure prediction | http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3/ | Default |
17 | PatchDock | Molecular docking algorithm based on shape complementarity principles | Default | |
18 | FireDock | Refinement and re-scoring of rigid-body protein-protein docking | Default | |
19 | ClusPro | Molecular docking | Default |