an epitope associates with which part of an antibody,an epitope is,antibody design,antibody epitope,antibody epitope mapping,antibody epitope prediction,antibody software,antigen and antigenicity,antigen and epitope,antigen database,antigen definition,antigen design,antigen epitope,antigen mapping,antigen software,antigenic determinant,antigenic determinant epitope,antigenic determinant site,antigenic peptide,antigenic peptide prediction tool,antigenicity,antigenicity and immunogenicity,antigenicity plot,antigenicity prediction,antigenics,b cell epitope,b cell epitope mapping,b cell epitope prediction,b cell epitope prediction server,bepipred linear epitope prediction,bepipred linear epitope prediction,conformational epitope,conformational epitope mapping,continuous epitope,define epitope,define immunogenic,difference between b cell epitope and t cell epitope,difference between epitope and paratope,discontinuous epitope,ellipro,epi 2.0,epiquest,epitool,epitope analysis,epitope and paratope,epitope based vaccines,epitope binding,epitope database,epitope definition,epitope diagnostics,epitope immunology,epitope mapping,epitope mapping methods,epitope mapping protocols,epitope mapping review,epitope mapping service,epitope mapping software,epitope meaning,epitope paratope,epitope prediction,epitope prediction methods,epitope prediction server,epitope prediction software,epitope prediction tools,epitope recognition,epitope sequence,epitope size,epitope structure,epitope types,epitope vaccine,epitope vs antigen,epitope y paratope,epitopes or antigenic determinants,epivax,expasy,expasy protparam,expasy tools,hydrophobicity prediction,iedb epitope prediction,immune database,immune epitope database,immunodominant epitope,immunogenic definition,immunogenic epitopes,immunogenic peptides,immunogenicity prediction,immunogenicity prediction software,immunogenicity prediction tool,in silico analysis of protein,in silico immunogenicity prediction,linear epitope,linear epitope prediction,linear vs conformational epitopes,mimotopes,paratope,paratope vs epitope,pepscan epitope mapping,peptide analysis tool,peptide antibody,peptide array,peptide calculator,peptide design,peptide epitope,peptide generator,peptide immunogenicity prediction,peptide mapping,peptide prediction,peptide vaccine examples,predict tool,predictive algorithms,proimmune,properties of b cell epitopes,protein analysis,protein analysis tools,protein epitope,protein hydrophobicity prediction,random peptide library,syfpeithi,syfpeithi epitope prediction,synthetic peptide vaccine,synthetic peptide vaccine,types of epitopes,viral epitope,what does epitope mean,what is an epitope

Predicting Immunogenicity of B-epitopes

Exhibit 1. Predicted and actual immunodominant epitopes of NS1 protein [Dengue virus]. To illustrate what EpiQuest-B can predict, the NS1 is one of the best examples, as its immunodominant epitopes were investigated with high precision and detail. In total, there are 8 immunodomiant epitopes covering 3 areas in the N-terminal part of the molecule. As can be seen, all 3 areas were detected by EpiQuest-B with high precision, as 3 main peaks in the antigenicity profile of the molecule.

Exibit 2 (on the right). What other algorithms find in the same sequence? We have compared the plots generated for NS1 by EpiQuest-B and by most prominent epitope/antigenicity defining programs available on the present day: Antigenicity by Kolaskar & Tongaonkar, BepiPred, and COBEPro. In Figure 2 the antigenicity propensity plot as obtained by current versions of the programs at the default settings. The position of the known immunodominant epitopes is indicated, and it is clear that EpiQuest is the only program that detects all three immunodominant epitopes areas as the highest values regions. Both algorithms of Kolaskar & Tongaonka, as well as antigenicity algorithm of COBEPro either miss the epitopes entirely or detect only part of them, ascribing the other part to low antigenicity areas (Fig. 2B, D). Bepiped seeks only for epitopes probability and it correctly exactly one of the immunodominant epitopes, although does not ascribe it a high value (Fig 2, C)

Exibit 3 (below). The antigenicity Index predicted by EpiQuest-B correlates with immunogenicity of the respective sequence with a high statistical significance.

The data are available on the titre of antibody response, as measured by ELISA, for several regions of NS1 (CLINICAL AND VACCINE IMMUNOLOGY, 2007, p. 493–504). Two strains of mice, of different haplotype, were immunized with several types of antigens (peptide, native NS1 or live DV2), and their pooled sera were tested against a set of overlapping peptides. We have defined AGI for the fragments, and have built correlation graphs for AGI vs ELISA data. 

EpiQuest™-B

In predicting B-epitopes, whether for the needs of antibody production or finding the areas, inducing the humoral response (for diagnostics), the main question is: whether this sequence is capable to elicit an immune response? Our research (Litvinov et al, in preparation) showed that the structure of peptide sequence defines the probability of a strong humoral response to it.

 

Based on our ideas of peptide-peptide interactions, a new algorithm employed in EpiQuest-B evaluates the potential immunogenicity of the peptide sequence. The software calculates the Antigenicity Index for a given sequence (AGI).

 

The higher the AGI, the more likely is the strong humoral response to it. This is something NONE of the existing epitope prediction software is capable of, while EpiQuest-B does it with a high statistical significance (see below).

The correlation is highly significant: the AGI index corresponds to the level of antibody response to the respective fragment, irrespective of whether the peptides, purified protein or even whole virus were used for immunization.

Epitope,epitope mapping, epitope prediction, antibody epitope, CTL epitope, T-cell epitope, immunogenic epitope, antigen antibody, antigenicity prediction, t cell epitope prediction, syfpeithi epitope prediction, prediction of secondary structure, protein analysis, protein sequence analysis, sequence analysis software, antigenicity prediction tool, peptide sequence, immunogenic peptide, structural analysis software, peptide mass, peptide charge, pI protein, isoelectric point peptide, peptide molecular weight calculator,protein sequence analysis, amino acid sequence, Epitope,epitope mapping, epitope prediction, antibody epitope, CTL epitope, T-cell epitope, immunogenic epitope, antigen antibody, antigenicity prediction, t cell epitope prediction, syfpeithi epitope prediction, prediction of secondary structure, protein analysis, protein sequence analysis, sequence analysis software, antigenicity prediction tool, peptide sequence, immunogenic peptide, structural analysis software, peptide mass, peptide charge, pI protein, isoelectric point peptide, peptide molecular weight calculator,protein sequence analysis, amino acid sequence, Epitope,epitope mapping, epitope prediction,antibody epitope, CTL epitope, T-cell epitope, immunogenic epitope, antigen antibody, antigenicity prediction, t cell epitope prediction, syfpeithi epitope prediction, prediction of secondary structure, protein analysis, protein sequence analysis, sequence analysis software, antigenicity prediction tool, peptide sequence, immunogenic peptide, structural analysis software, peptide mass, peptide charge, pI protein, isoelectric point peptide, peptide molecular weight calculator,protein sequence analysis, amino acid sequence, Epitope,epitope mapping, epitope prediction, antibody epitope, CTL epitope, T-cell epitope, immunogenic epitope, antigen antibody, antigenicity prediction, t cell epitope prediction, syfpeithi epitope prediction, prediction of secondary structure, protein analysis, protein sequence analysis, sequence analysis software, antigenicity prediction tool, peptide sequence, immunogenic peptide, structural analysis software, peptide mass, peptide charge, pI protein, isoelectric point peptide, peptide molecular weight calculator,protein sequence analysis, amino acid sequence, Epitope,epitope mapping, epitope prediction, antibody epitope, CTL epitope, T-cell epitope, immunogenic epitope, antigen antibody, antigenicity prediction, t cell epitope prediction, syfpeithi epitope prediction, prediction of secondary structure, protein analysis, protein sequence analysis, sequence analysis software, antigenicity prediction tool, peptide sequence, immunogenic peptide, structural analysis software, peptide mass, peptide charge, pI protein, isoelectric point peptide, peptide molecular weight calculator,protein sequence analysis, 

an epitope associates with which part of an antibody,an epitope is,antibody design,antibody epitope,antibody epitope mapping,antibody epitope prediction,antibody software,antigen and antigenicity,antigen and epitope,antigen database,antigen definition,antigen design,antigen epitope,antigen mapping,antigen software,antigenic determinant,antigenic determinant epitope,antigenic determinant site,antigenic peptide,antigenic peptide prediction tool,antigenicity,antigenicity and immunogenicity,antigenicity plot,antigenicity prediction,antigenics,b cell epitope,b cell epitope mapping,b cell epitope prediction,b cell epitope prediction server,bepipred linear epitope prediction,bepipred linear epitope prediction,conformational epitope,conformational epitope mapping,continuous epitope,define epitope,define immunogenic,difference between b cell epitope and t cell epitope,difference between epitope and paratope,discontinuous epitope,ellipro,epi 2.0,epiquest,epitool,epitope analysis,epitope and paratope,epitope based vaccines,epitope binding,epitope database,epitope definition,epitope diagnostics,epitope immunology,epitope mapping,epitope mapping methods,epitope mapping protocols,epitope mapping review,epitope mapping service,epitope mapping software,epitope meaning,epitope paratope,epitope prediction,epitope prediction methods,epitope prediction server,epitope prediction software,epitope prediction tools,epitope recognition,epitope sequence,epitope size,epitope structure,epitope types,epitope vaccine,epitope vs antigen,epitope y paratope,epitopes or antigenic determinants,epivax,expasy,expasy protparam,expasy tools,hydrophobicity prediction,iedb epitope prediction,immune database,immune epitope database,immunodominant epitope,immunogenic definition,immunogenic epitopes,immunogenic peptides,immunogenicity prediction,immunogenicity prediction software,immunogenicity prediction tool,in silico analysis of protein,in silico immunogenicity prediction,linear epitope,linear epitope prediction,linear vs conformational epitopes,mimotopes,paratope,paratope vs epitope,pepscan epitope mapping,peptide analysis tool,peptide antibody,peptide array,peptide calculator,peptide design,peptide epitope,peptide generator,peptide immunogenicity prediction,peptide mapping,peptide prediction,peptide vaccine examples,predict tool,predictive algorithms,proimmune,properties of b cell epitopes,protein analysis,protein analysis tools,protein epitope,protein hydrophobicity prediction,random peptide library,syfpeithi,syfpeithi epitope prediction,synthetic peptide vaccine,synthetic peptide vaccine,types of epitopes,viral epitope,what does epitope mean,what is an epitope

Exhibit 4. Correlation of predicted and actual immunodominant epitopes for Ro ribonucleoprotein [human autoantigen, GenBank: AAA35493.1] Finally, we show an illustration of EpiQuest performance with the sequence where multiple epitopes of different immunogenicity are known. All known (immunodominant and weak) B-epitopes were established for Ro autoantigen. On the presented profile of the protein immuogenicity there is a peak corresponding to every epitope detected experimentally in Ro molecule. Two peaks (marked xx) that do not correspond to known epitopes, are within the inaccessible area of the molecule.

EpiQuest, 12 month individual subscription

for academia, government research facilities and non-profit organizations

#AP0300012    .....................   GBP 415.-

© 2013, 2015,2018  by APTUM BIOLOGICS LTD.