VaxiJen protocols

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VaxiJen statistics

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VaxiJen specifications

Information


Unique identifier OMICS_12403
Name VaxiJen
Interface Web user interface
Restrictions to use None
Input data Protein sequence
Input format Plain format or fasta
Programming languages Perl
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Publication for VaxiJen

VaxiJen in pipelines

 (6)
2017
PMCID: 5450251
PMID: 28584450
DOI: 10.6026/97320630013094

[…] a prediction that is based on the sequence and features of amino acids and their properties., the identified epitope(s) were used to predict whole protein antigenicity (protective antigen) using vaxijen 2.0 server program with a threshold limit of 0.5 []. the threshold values of the highest accuracy of more than 0.5 were considered probable antigens and were selected for further analysis. […]

2017
PMCID: 5569093
PMID: 28835708
DOI: 10.1038/s41598-017-09199-w

[…] prediction is −0.40. prediction score less than threshold value point towards the non-allergic behavior of peptide. antigenicity of vaccine construct was predicted using antigenpro and followed by vaxijen 2.0. the predicted antigenicity probability from antigenpro was 0.830426 which shows a good antigenic nature of vaccine construct. overall prediction for the antigen was performed by using […]

2017
PMCID: 5602290
PMID: 28943728
DOI: 10.6026/97320630013231

[…] a prediction that is based on the sequence and features of amino acids and their properties., the identified epitope(s) were used to predict whole protein antigenicity (protective antigen) using vaxijen 2.0 server program with a threshold limit of 0.5 []. the threshold values of the highest accuracy of more than 0.5 were considered probable antigens and were selected for further analysis., […]

2016
PMCID: 4742598
PMID: 26866023
DOI: 10.7774/cevr.2016.5.1.41

[…] were used for prediction of continuous and discontinue b-cell epitopes, respectively. mhc super type a1 by netctl 1.2 server (http://www.cbs.dtu.dk/services/netctl/). finally, we used the vaxijen server to predict the immunogenicity of the whole tetravalent fusion protein (http://www.ddg-pharmfac.net/vaxijen/vaxijen/vaxijen.html)., a multi-step immunoinformatic approach was used […]

2016
PMCID: 5091093
PMID: 27812281
DOI: 10.4137/DTI.S38458

[…] information (ncbi). the 3d structure of hla was obtained from research collaboratory for structural bioinformatics (rcsb). online and offline software including the latest version of bcpred, vaxijen v2.0, paproc i, tappred,, immune epitope database (iedb) 3.0, pep-fold, moe 2009, and chimera 1.9 were used in this study., the sequences of polysaccharide protein of s. pneumoniae, n. […]


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VaxiJen in publications

 (55)
PMCID: 5954444
PMID: 29780242
DOI: 10.1177/1177932218755337

[…] of the 6 approaches can be used to predict the allergenic proteins with high precision., to verify antigenicity of the proteins and the peptides predicted by the tools, 2 software were applied. the vaxijen v2.0 software (available at http://www.ddg-pharmfac.net/vaxijen/vaxijen/vaxijen.html) works based on independent alignment prediction of protective antigens. this software was developed […]

PMCID: 5915591
PMID: 29691454
DOI: 10.1038/s41598-018-24674-8

[…] made for 8–14 mer peptides of mhc i and 15 mer peptides of mhc ii for analysis,,. the conservancy of epitopes and antigenicity were determined by immune epitope database analysis resource (iedb) and vaxijen score., leptospiral bacterins, whole cell lysate (wcl) were prepared from leptospira interrogans serovar autumnalis strain n2 as previously described. reca or flid recombinant proteins […]

PMCID: 5879067
PMID: 29032659
DOI: 10.4142/jvs.2018.19.2.188

[…] solved three-dimensional structures were determined by using the protein data bank (pdb, usa) [] and modbase [], respectively. to predict the protective antigens and subunit vaccines, vaxijen v2.0 was used []., drugbank (ver. 4.3) [], which contains unique bioinformatic and cheminformatic data on drugs and drug targets, was used to determine the druggability of the identified […]

PMCID: 5761135
PMID: 29316918
DOI: 10.1186/s12936-017-2144-x

[…] with a size of 20 aminoacids, set to a 75% specificity. after identifying the best predicted epitopes based on score, each of these epitopes was screened for predicted antigenicity using the vaxijen v.2 software [], under a 0.5 threshold and the “parasite model” filter on, according to previously published recommendations [, ]. subsequently, all epitopes presenting scores above 0.5 […]

PMCID: 5712781
PMID: 29225429
DOI: 10.6026/97320630013366

[…] of viruses., dimitrov et al. [] reported a systematic platform for prediction of immunogenicity and mhc class i binding affinity. the platform integrates three quasi-independent modular servers: vaxijen for immunogenicity and epijen to predict peptide binding to mhc class i proteins. we however used mhc prediction first to identify as many epitopes as possible followed by screening […]


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VaxiJen institution(s)
Faculty of Pharmacy, Medical University of Sofia, Sofia, Bulgaria; The Jenner Institute, Oxford University, Compton, Berkshire, UK
VaxiJen funding source(s)
The present study was supported in part by grants from the Royal Society, UK, and the Ministry of Education and Science, Bulgaria.

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