epitope prediction and protein analysisePitope InformaticsePitope Informatics

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 


ePitope Informatics is an applied bioinformatics company providing services for epitope discovery. A particular focus is epitope prediction for the identification and targeting of antibody epitopes.
 

ON THIS PAGE
Epitope prediction

Related protein annotation

Consensus epitope prediction Further epitope analysis
3-D structure analysis e-Report Hardcopy report Future services

 

 Protein services at a glance
 
  Consensus epitope
  prediction
(B cell)
  • Antigenicity (3 algorithms).
  • Flexibility (1 algorithm).
  • Hydrophilicity (2 algorithms).
  • Hydrophobicity (5 algorithms).
  • 2 structure prediction (2 algorithms)
  • Beta-turn structure analysis.
  • PROSITE pattern motif searching.
  • Further relevant protein analysis.
  • Rank of epitopes as likely antigens.
 
   
  Epitope mapping to target
  protein 3-D structure
  • Degree of epitope surface exposure.
  • Association with beta-turn structures
  • Conformational epitopes.
  • Rank of epitopes as likely antigens.

 

Epitope prediction

Our initial approach to epitope prediction (B cell) includes use of the
multiple algorithms, and an easy-to-follow explanation of each algorithm
is provided with commercial service e-Reports).

Related protein annotation and analysis

Late-night epitope prediction

Our service includes:

  Epitope mapping to solved or modelled protein 3-D
   structure (if available) - see below.

  Identification of amino acid sequence pattern motifs (PROSITE).

  Reviewing available published literature and specialist protein
    databases
for further information relating to your target protein
   and predicted epitopes.

  Comment on N- and C-terminus regions.

  The effect of varying algorithm window size (where applicable).

  Prediction of transmembrane spanning regions.

  Signal/cell sorting sequence prediction.

  PEST sequence analysis.

  Target protein physicochemical properties.

  Recommendations for epitope peptide synthesis and
    conjugation to carrier protein
.

 

Consensus epitope prediction

ePitope Informatics uses algorithm profiling combined with other
information we obtain (as above) to identify and rank consensus predicted epitopes. From this analysis, we generate a list of consensus predicted epitopes, ranked in order of their likely antigenicity.

This data is included in our service e-Report (see below).

Consensus predicted epitopes show:

High values for predicted antigenicity, flexibility and surface
        location.

A high degree of association with predicted β-turns (secondary
        structures frequently associated with antigenic sites,
        particularly when they are adjacent to β-sheets or
α-helical
        structures, in regions of hydrophilicity and flexibility).

Low hydrophobicity and high hydrophilicity values. However,
        not all antigenic sites are hydrophilic, hence the value of
        applying the above algorithms in a consensus approach to
        epitope prediction.
 

Further epitope analysis

For each target protein we offer further analysis of up to four
consensus predicted epitope sequences that can include investigation of:

Epitope location on solved or modelled target protein 3-D
        structure (if available).

We can select, for further analysis, any identified target protein subsequence regions and/or consensus predicted epitopes of interest.

Further analysis can provide:

Information that can aid, possibly even greatly influence,
        which epitopes are chosen for use in further work.

Additional molecular biological characterisation and annotation
        of the target protein.

Additional information that can be utilised downstream in
        research projects.


 

Analysis of target protein 3-D structure

We map predicted antibody epitopes to the solved 3-D structure of a target protein (if available), and report on epitope location in relation to other protein structural and functional sites. Modelling potentially antigenic regions to protein 3-D structure increases the accuracy of epitope prediction, and assists determining epitope boundaries. It also aids identification of predicted discontinuous ("conformational") epitopes.

If a solved 3-D structure is not available, there is an option for either us or the client to provide an identity/homology modelled structure for epitope analysis.

Our molecular modelling platform includes use of high performance graphics workstations and stereoscopic 3-D viewing hardware (from NVIDIA and StereoGraphics/RealD), and a variety of software that includes Discovery Studio from BIOVIA (formerly Accelrys).

This platform allows our introduction of enhanced molecular analysis and modelling services for antibody epitope prediction and mapping to protein 3-D structure, which includes identification and contextual characterisation of both linear and discontinuous ("conformational") epitopes, and protein comparative modelling services.

For up to six consensus predicted epitopes, we report on their degree of surface location, surface exposure of component amino acids, and epitope association with β-turns. β-turns are secondary structures frequently associated with antigenic sites, particularly when they are adjacent to β-sheets or α-helical structures in regions of hydrophilicity and polypeptide chain flexibility. We also report on association of predicted epitopes with other regional features indicating a site of potential antigenicity.

Our service report also provides high quality colour images of different target molecule 3-D views, annotated with predicted epitopes. These Figures show labelling of surface exposed (≥ 30%)epitope amino acids and peak predicted antigenic residues.

A similar analysis was used to construct the animated and
non-animated images showing predicted epitopes (peak regions only) at the surface of the human DNA repair protein, MGMT, shown on our Home page (and elsewhere on this site).

Then we rank identified surface-located epitopes on the basis of
a combination of their:

rank as a consensus predicted epitope.

degree of surface exposure.

association with β-turns and other regional features
         indicating a site of potential antigenicity.
 

e-Report and secure delivery

We send an e-Report as part of all commercial services.

e-Reports are encrypted password-protected Adobe PDF files that are sent by standard e-mail or secure e-mail (click here for more details), or by courier delivery on a disk.

We use the Adobe PDF format as it allows enhanced document security and can be accessed across nearly all computer operating systems.

e-Reports are about 50 pages in length, and are enabled with Adobe Acrobat bookmarks (to aid their navigation), active hyperlinks and other attributes.

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

e-Reports set out the results obtained from the above analysis of the target molecule of interest, in mixed text and graphics format. This includes our annotation of the target molecule's primary sequence with predicted epitope sequences and protein secondary structure. If analysis of 3-D structure has been performed, the e-Report will contain output showing actual (in addition to predicted) secondary structure of the target protein.

Protein 3-D structure analysis provides a series of graphics images showing the target molecule annotated with up to 6 consensus predicted epitopes. These images highlight surface-located, partially exposed and buried residues, and  β-turns associated with each epitope.

e-Reports, which are optimally viewed using the latest version of Adobe Acrobat Reader (version 6.x onwards required), initially are disabled for printing (and for selecting text and graphics). These functions are enabled once invoice payment has been made (see "Payment" section).



 

Future services

One of our goals is to remain relevant to scientists' needs by responding constructively to feedback. Therefore, we would appreciate any input you are willing to share regarding services we might provide in the future. Possible future service options include:

Antibody-antigen interaction analysis (docking/molecular dynamics).

T cell epitope prediction and analysis.
 

 

 

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Copyright 2017 ePitope Informatics

 

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

 

 

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