Designing of Potential Polyvalent Vaccine Model for Respiratory Syncytial Virus by System Level Immunoinformatics Approaches

Table 1

Databases/tools/servers used for the design of RSV polyvalent vaccines.

Databases/tools	Web link	Purpose	Reference
NCBI	https://www.ncbi.nlm.nih.gov/	Data accession	—
VaxiJen server	http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html	Antigenicity prediction	[21]
Virus-mPLoc	http://www.csbio.sjtu.edu.cn/bioinf/virus-multi/	Subcellular localization	[19, 20]
HADDOCK 2.2	https://haddock.science.uu.nl/	Epitope docking	[31]
ProPred	http://Crdd.osdd.net/raghava/propred/	MHC class II epitope prediction	[60]
Propred1	http://crdd.osdd.net/raghava/propred1/	MHC class I epitope prediction	[22]
IEDB (NetChop)	http://tools.iedb.org/netchop/result/	Proteasomal cleavage analysis	[44]
IEDB	http://tools.iedb.org/conservancy/	Epitope conservational studies	[23]
PEPFOLD	http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD/	Epitopes 3D modeling	[24]
Cytoscape	http://www.cytoscape.org/	Protein-protein interaction	[61]
MOE	https://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm	Epitopes affinity prediction	—
ITASSER	https://zhanglab.ccmb.med.umich.edu/I-TASSER/	3D modeling	[26, 62, 63]
Chimera	https://www.cgl.ucsf.edu/chimera/	Protein visualization	[64]
Qmean	https://swissmodel.expasy.org/qmean/	Quality estimation	[65]
Rampage analysis	http://mordred.bioc.cam.ac.uk/~rapper/rampage.php	Confirmation of amino acids	[66]
3D refine	http://sysbio.rnet.missouri.edu/3Drefine/	Protein refinement	[67–69]
Antigen pro	http://scratch.proteomics.ics.uci.edu/explanation.html#ANTIGENpro	Prediction of antigenicity	[70]
VaxiJen	http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html	Prediction of antigenicity	[21, 71]
AllergenFP	http://www.ddg-pharmfac.net/AllergenFP/	Predicting Allergenicity	—
AlgPred	http://crdd.osdd.net/raghava/algpred/submission.html	Predicting Allergenicity	—
Sol pro	http://scratch.proteomics.ics.uci.edu/explanation.html#SOLpro	Solubility prediction	[70]
PROSO	http://mbiljj45.bio.med.uni-muenchen.de:8888/proso/proso.seam	Prediction of solubility	[72]
Expasy	http://web.expasy.org/compute_pi/	Molecular weight prediction	[73, 74]