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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 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