Skip to main content

Table 1 Details of the computational tools used for the prediction of antigens, epitopes and their population coverage analysis

From: Exploitation of reverse vaccinology and immunoinformatics as promising platform for genome-wide screening of new effective vaccine candidates against Plasmodium falciparum

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 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