Protein epitope prediction and analysisePitope InformaticsePitope Informatics

 

 

 

 

 

 

 

The problem

You might be a research scientist wishing to make a peptide and antibody for probing a protein's structure and function, or one developing a vaccine or an immunodiagnostic test, or you might be an antibody producing company wishing to expand its product portfolio.

At the outset of any of these pursuits, possibly the most frequently expressed concern is which peptide sequences to choose for generating antibodies.

Alternatively, you may be experiencing difficulty producing antibodies to a purified protein and even be considering artificially tagging the target protein with an unrelated epitope.

Or, you may be frustrated by the lack of commercially available antibodies to regions other than protein N- and C-termini, and, thus, be considering producing your own antibodies.

You may even wish to produce a library of peptides and antibodies to target specific regions of a protein of interest.

Also, you may be unsure of the thoroughness of an epitope prediction service that is bundled with a peptide synthesis or epitope mapping service.

In any of these situations you might be faced with choosing between self-performed epitope prediction and analysis, which is difficult, or enlisting assistance from experts such as ePitope Informatics.

 

 

ePitope Informatics    

 

 

 

Our solution

ePitope Informatics specialises in in silico epitope discovery and related protein annotation, with a particular focus being epitope prediction and target protein epitope contextual analysis for the identification and targeting of antibody epitopes.  ePitope Informatics is also research-active in these areas.

Our solution is to provide in silico  epitope discovery services that address issues including:

Epitope prediction
          accuracy,
and the
        evidence that it is better to
        arrive at a consensus
        through use a variety of
        algorithms and structure
        prediction approaches.

The evidence for certain
           epitope prediction
           algorithms being better
           than others
.

Ranking predicted
          epitopes
in order of likely
        antigenicity.

Weighting given to a
         region predicted to be
         surface located but not
         predicted to be antigenic,
         or vice versa.

Optimal "window"
           settings
of certain
         algorithms, and the
         possibility of adjusting
         these (which changes the
         "smoothing effect" of
            the algorithm
) to obtain
          extra information.

Degree of importance
        attached to findings of
          secondary structure
          prediction
.

Analysing predicted
        epitopes located on solved
          3-D structures
.

The presence of amino
          acid sequence motifs and
          protease cleavage sites
        
 providing further evidence
        that a predicted epitope is
        surface-located on a target
        protein.

Possible antibody
          cross-reactivities
        
 identified by searching
          primary protein
          databases
for sequences
        showing identity to
        predicted epitopes.

The effect of low
          complexity regions
        
 (in epitope query
        sequences) on primary
        protein database searching.

Primary protein database
        search parameters that are
        recommended for use with
          shorter query strings
       
 (e.g. predicted epitopes).

Sequence gaps
          (insertions and
          deletions)
in returned
          sequence alignments
        
 from primary protein
        database searches.

Frequently occurring
           amino acid signature
           sequences
in primary
         protein databases and
         predicted epitope query
         sequences, which can
         cause important
         alignments to be missed.

 

What you get

An extensive, high quality e-Report, with all of our epitope
        prediction and analysis services, and normally within 2 weeks of
        order confirmation.


The main report (50 - 60 pages), which begins with a summary
          
of our findings, and ends with conclusions and
           recommendations
, is a PDF file, Adobe-bookmarked for easy
         navigation, and packed with easy-to-follow explanation of
           the epitope prediction and analysis data
we provide.


All service e-reports ("full service report" and "simple list of
        epitopes service report") are provided with support documentation
        describing protein database searching optimised for use with
        predicted epitopes as search query strings.


 

click here for further details of our services.

 

 

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Copyright 2017 ePitope Informatics


epitope prediction
Consensus epitope prediction
(Human DNA
 repair protein,
 MGMT - peak
 epitope residues
 shown in gold).

 

 

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