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
prediction (B cell)
- Antigenicity (3
- Flexibility (1
- 2° structure prediction (2 algorithms)
- Beta-turn structure analysis.
- PROSITE pattern
relevant protein analysis.
- Rank of
epitopes as likely antigens.
Epitope mapping to target
protein 3-D structure
- Degree of
epitope surface exposure.
with beta-turn structures
- Rank of
epitopes as likely antigens.
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
Our service includes:
mapping to solved or modelled
structure (if available) - see below.
Identification of amino acid sequence
pattern motifs (PROSITE).
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.
Recommendations for epitope peptide synthesis
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
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
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
Further epitope analysis
For each target protein we offer further analysis of up to four
consensus predicted epitope sequences that can include investigation of:
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
Further analysis can
Information that can aid, possibly even greatly influence,
which epitopes are chosen for use in
molecular biological characterisation and annotation
of the target protein.
information that can be
utilised downstream in
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.
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).
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
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
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
e-Report and secure
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
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
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:
interaction analysis (docking/molecular dynamics).
T cell epitope prediction and analysis.
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