Protein epitope prediction and 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.
 

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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 further analysis
  • BLASTP database searching
    (optimised for epitope queries).
  • Protease cut-site mapping
    (for epitope mapping/protein digestion, sequencing, MS analysis).
 
   
Epitope mapping to target protein solved or modelled 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
following algorithms (an easy-to-follow explanation of each algorithm
is provided with commercial service e-Reports):

Protein antigenicity prediction algorithms

    Parker

    Protrusion Index (Thornton)

    Hopp and Woods

Protein hydrophobicity algorithms

    Kyte and Doolittle

    Janin

    Sweet and Eisenberg

    Manavalan

    Fauchere

Protein hydrophilicity algorithms

    Goldman, Engelman and Steitz (GES)

    von Heijne

Protein flexibility prediction algorithm

    Karplus and Schulz

Protein secondary structure prediction
        algorithms

    Garnier and Robson

    Chou and Fasman

       

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 identity to databased protein sequences.

Epitope (and flanking region) protease cleavage sites.

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.


More detail

Database searching
ePitope Informatics uses BLAST (Basic Local Alignment Search Tool), specifically BLASTP, to search the nr protein database, a composite protein sequence database held at the National Centre for Biotechnology Information (NCBI). The nr database is a composite of all non-redundant GenBank CDS translations, PDB, SwissProt, PIR and PRF databases. These searches, which are performed from within Accelrys Discovery Studio software for a maximum of 4 consensus predicted epitopes, retrieve sequences showing identity to consensus predicted epitopes. In this manner you will be made aware of possible cross-reactivity with another protein that an antibody to a particular epitope sequence might show.

Protease cut-site mapping
We analyse consensus predicted epitopes and flanking sequences for
the presence of protease cleavage sites, using an in-house extendeded version of the composite PABASE database of proteases included within OMIGA™ 2.0 software (Accelrys; click here for list of proteases). Protease cut-site analysis can be used for downstream epitope mapping/protein digestion, sequencing and MS analysis, and is performed for a maximum of 4 consensus predicted epitopes.

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.

New graphics workstations and stereoscopic 3-D viewing  hardware (StereoGraphics CrystalEyes® 3 and related hardware from Real D Corporation), for use with Discovery Studio software from Accelrys, allows our introduction of enhanced molecular modelling services for  linear and discontinuous epitope prediction and mapping to protein 3-D structure and comparative protein modelling.

Currently, we perform protein 3-D analysis using several molecular
3-D viewing programs including Discovery Studio software from Accelrys. 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 of epitope prediction and analysise-Report

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

We send e-Reports (in Adobe PDF format) via the Internet by Tumbleweed Secure Messenger (free of charge). e-Report package PDF files can also be delivered by standard e-mail or secure e-mail (click here for more details), or sent on a disk. Files sent by standard e-mail or on a disk will be password protected and encrypted.

e-Reports are in Adobe PDF format. We use this format as it can be
accessed across nearly all computer operating system platforms (e.g.
Windows, Mac, and most versions of Unix). e-Reports are about 50
pages in length, and are enabled with Adobe Acrobat bookmarks (to
aid their navigation) and active hyperlinks. Please note that the on-
screen version of your e-Report does not yield as high a resolution as
the printed copy.

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.

Consensus predicted epitopes subjected to further analysis (see
above) are annotated with protease cut-sites, amino acid sequence
motifs, and predicted secondary structure obtained from output
derived for the whole molecule. In addition, if 3-D structure analysis
has been performed, the e-Report will contain output showing
actual (in addition to predicted) secondary structure of the target protein.

Further output provided can include nice-view-like lists of databased
protein alignments (usually 100 - 300 per epitope), and cut-sites for
the 120 proteases in our database. Due to their large page length,
this output is supplied as extra PDF files in addition to the main
report PDF file.

Target protein 3-D structure analysis provides a series of graphics
images of the solved 3-D structure of your molecule of interest,
annotated with up to 6 consensus predicted epitopes. This
output also shows surface-located, partially exposed, 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 service payment has been received (see
"Payment" section).


 

Optional hardcopy report

In Hardcopy report of epitope prediction and analysisaddition, we offer you the option of ordering a hardcopy version
of this report, printed in colour and black and white
on high quality, "bright white" paper, and loosely
bound in a plastic report folder. This is a printout
of the main report PDF file in the e-Report package
we send you.

Printed reports does not include hardcopy of the
content of extra PDF files in an e-Report package (see above).
In the instance of a hardcopy report alone being ordered (i.e. no e-
Report), these extra PDF files will be sent to you along with the
hardcopy report on a disk. Files on the disk will be password protected and encrypted.

Hardcopy reports are couriered by FedEx or DHL, with a signature
required on delivery for security. We notify you by e-mail when
reports have been despatched, and we give you a Waybill Number
that allows you to track delivery door-to-door via the Web.

FedEx logo

 

Future services

One of our goals is to remain relevant to scientists' needs by
constructively responding 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:

Protein identity/homology modelling.*

T cell epitope prediction and analysis.
 

*Can now be provided as part of a client-tailored service.

 

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This page was last updated:
Wednesday June 16, 2010

 

Copyright © 2000 - 2010 ePitope Informatics

 

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

 

 

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