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 | http://www.cbs.dtu.dk/services/SignalP/ | Default |
| 2 | PredGPI | Prediction system for GPI-anchored proteins | http://gpcr.biocomp.unibo.it/predgpi/pred.htm | Default |
| 3 | MAAP | Prediction of Malarial adhesins and adhesins-like proteins. | http://maap.igib.res.in/ | ≥ 0 |
| 4 | TMHMM2.0 | Transmembrane helices in the integral membrane proteins | http://www.cbs.dtu.dk/services/TMHMM/ | ≤ 1 |
| 5 | VaxiJen2.0 | Prediction of protective antigens | http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html | ≥ 0.5 |
| 6 | ExPASy-ProtParam | Calculation of physicochemical parameters | https://web.expasy.org/protparam/ | Default |
| 7 | MAFFT7.0 | Multiple sequence alignment | http://mafft.cbrc.jp/alignment/server/large.html. | Default |
| 8 | INNOVAGEN | Prediction of water solubility of proteins | https://pepcalc.com/ | Default |
| 9 | IEDB-MHC class I-Consensus | Prediction of MHC class I binding epitopes | http://tools.iedb.org/mhci/ | IC50 ≤ 500 nM |
| 10 | IEDB-MHC class II-Consensus | Prediction of MHC class II binding epitopes | http://tools.iedb.org/mhcii/ | ≤ 3 percentile rank |
| 11 | IEDB-Population Coverage | Population coverage analysis of selected epitopes | http://tools.iedb.org/population/ | Default |
| 12 | CTLPred | Prediction of cytotoxic T cell epitopes | http://crdd.osdd.net/raghava/ctlpred/ | Default |
| 13 | IL-10Pred | Prediction of IL-10 inducer epitopes | http://webs.iiitd.edu.in/raghava/il10pred/predict3.php | Default |
| 14 | TAPPred | Prediction of TAP binding affinity of epitopes | http://crdd.osdd.net/raghava/tappred/ | Default |
| 15 | IFNepitope | Prediction of IFN-γ inducer epitopes | http://crdd.osdd.net/raghava/ifnepitope/predict.php | 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 | https://bioinfo3d.cs.tau.ac.il/PatchDock/ | Default |
| 18 | FireDock | Refinement and re-scoring of rigid-body protein-protein docking | http://bioinfo3d.cs.tau.ac.il/FireDock/ | Default |
| 19 | ClusPro | Molecular docking | https://cluspro.bu.edu/login.php | Default |