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"When selecting an epitope for antibody response, one would like to know its immunogenicity. 

We know how to predict it..."

Analysis of protein sequence for the presence of continuous linear epitopes still greatly lags behind i.e. the prediction of potential T-cell epitopes. In part this may be related to a quite unclear definition of what one considers an epitope. Most of the current prediction software estimates the probability of a particular peptide within the sequence being exposed at the surface of the molecule encoded by analysed sequence.

Very few prediction programs (i.e. Algorithm of Kolaskar & Tongaonkar, algorithm of BCPreds) try to access the antigenicity of the potential epitopes.

The necessity to define potential epitope within the sequence is usually required for:

- To define the best peptide sequence in order to prepare a specific antibody to a particular molecule;

- To find sequences for most likely immune response by the host (to predict sites for autoimmune response or immune response against a particular foreign antigen, such as virus of bacteria in order to detect this response for diagnostic purposes)

- To find the sequences most likely to be a target for effective antibody response when designing the vaccines, especially multivalent ones where several antigenic modalities will compete for the attention of the host’s immune system.

As one can see, the real aim of analysing the sequence in order to define the best epitope lies in defining its immunogenicity; the question of surface exposure, however important comes as a second one.

What one is really interested in is defining “strong epitopes” capable to elicit high affinity antibodies in most of the hosts.



EpiQuest™ 2014

EpiQuest is a registered Trademark of Aptum Biologics Ltd.

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EpiQuest is a unique software suite for analysis of linear protein sequence for the presence of B-cell, T-cell epitopes, area complexity (immunological, functional). It is based on new algorithms developed by Aptum Bio, and so far is unparalleled by other software.


To learn more, please follow to our specialised site:


Find B-cell epitopes and evaluate their immunogenicity


To illustrate the crucial difference of EpiQuest from the most prominent b-epitope predicting software, we used one of the molecules, the NS1 protein of Dengue virus 2, as an example. The immunogenicity of this molecule has been studied in detail, and immunodominant epitopes were defined.

Comparison of values plots for NS1 protein. The plots were obtained by analysing the sequence (380aa) using EpiQuest-B 2.1.16 (A), Kolaskar & Tongaonkar antigenicity (B), BepiPred 1.0b epitope mapping (C) and  predicted antigenicity propensity score by COBEPro (D). The plots are presented for the entire sequence of NS1 (380aa). The default parameters for analysis were used. Red blocks indicate positions of 3 established epitopes of NS1, immunodominant in humans. Please note the correspondence of peaks, as detected by every programm, to the actual areas of immunodominant epitopes.

The program performs analysis of the given sequence and detects potentially immunodominant linear peptides. Non only it does this, but also assigns to peptides so-called AGI (antigenicity index), so that you can choose the best, and most immunogenic in particular species, as antigen for your future antibody.

It also allows you to predict at least some (mostly immunodominant) linear epitopes  within the sequence that will be used by a particular species for immune response.

EpiQuest-B program was designed to detect within the linear sequence (presented in FASTA) areas of the highest probability to be immunogenic in a host. At the current stage the matrix is based on immunogenicity for humans, mice and rabbits.


at a glance

While we are preparing a version of EpiQuest available online, you can already benefit from this technology through our Protein Analysis Services.

We will help you to find the best, unique and immungenic antigen. Some projects are eligible for a free analysis, please inquire. Corporate clients are advised to contact us for corporate clients pricing.

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