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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.
Protein services at a glance
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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.
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Epitope further analysis |
- BLASTP database
searching
(optimised for epitope queries).
- Protease
cut-site mapping
(for epitope mapping/protein digestion, sequencing, MS analysis).
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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.
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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):
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 Protein antigenicity prediction algorithms
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Parker |
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Protrusion Index (Thornton) |
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Hopp and Woods |
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Protein hydrophobicity algorithms
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Kyte and Doolittle |
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Janin |
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Sweet and Eisenberg |
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Manavalan |
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Fauchere |
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Protein hydrophilicity algorithms
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Goldman, Engelman and Steitz (GES) |
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von Heijne |
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Protein flexibility prediction algorithm
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Karplus and Schulz |
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Protein secondary structure prediction
algorithms
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Garnier and Robson |
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Chou and Fasman |
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Related protein annotation and analysis
Our service includes:
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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 .
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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
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
 addition, 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.
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
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