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BioMed Research International
/
2021
/
Article
/
Tab 1
/
Research Article
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
]