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. 2010:2010:297505.
doi: 10.1155/2010/297505. Epub 2010 Jul 4.

Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development

Yongqun He  1 , Zuoshuang Xiang, Harry L T Mobley
Affiliations

Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development

Yongqun He et al. J Biomed Biotechnol. 2010.

Abstract

Vaxign is the first web-based vaccine design system that predicts vaccine targets based on genome sequences using the strategy of reverse vaccinology. Predicted features in the Vaxign pipeline include protein subcellular location, transmembrane helices, adhesin probability, conservation to human and/or mouse proteins, sequence exclusion from genome(s) of nonpathogenic strain(s), and epitope binding to MHC class I and class II. The precomputed Vaxign database contains prediction of vaccine targets for >70 genomes. Vaxign also performs dynamic vaccine target prediction based on input sequences. To demonstrate the utility of this program, the vaccine candidates against uropathogenic Escherichia coli (UPEC) were predicted using Vaxign and compared with various experimental studies. Our results indicate that Vaxign is an accurate and efficient vaccine design program.

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Figures

Figure 1
Figure 1
The Vaxign algorithm pipeline.
Figure 2
Figure 2
ROC curve analysis of epitopes binding HLA A*0201.
Figure 3
Figure 3
Vaxign prediction of UPEC vaccine targets. (a) Selection of E. coli CFT073 as a seed genome. Different filter options are applied: only outer membrane proteins, maximum of one transmembrane helix, minimum adhesin probability of.51, having orthologs in other three UPEC genomes but no orthologs in K-12 strain M1655, and no similarity to any human or mouse proteins. (b) In total 22 proteins were predicted to meet selected criteria. (c) Detailed results for a particular protein, for example, NmpC. MHC Class I and II epitope prediction results are also available and can be further filtered. (d) Prediction of α-helices and their possible cellular locations of NmpC. (e) Prediction of β-barrels and their possible cellular locations of NmpC.
Figure 4
Figure 4
Prediction of UPEC vaccine targets conserved in four sequenced UPEC genomes using Vaxign. Note: * Co-ed represents the conserved proteins.
See this image and copyright information in PMC

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