Conformational Epitope Prediction Server

Developed@Bioinformatics Centre, University of Pune, INDIA

Bioinfo@Uop CE Server Help


Guided Tour: html format   png format

What are epitopes?
Types of Epitopes  
Existing Approaches to predict B-cell epitopes
CE Algorithm
Software details
System requirements
CE Home Page
Input/Output files and their Formats
Algorithm development  and contact details


What are epitopes?

The identification of the regions of interaction between an antigen (Ag) and an antibody (Ab) is one of the most interesting problems in molecular immunology. Antigen-antibody (Ag-Ab) complexes are non-obligatory heterocomplexes that are made and broken according to the environment or the external factors and involve proteins (antigen and antibody) that must also exist independently. The most remarkable feature of antigen-antibody interactions is the high affinity and strict specificity of antibodies for their antigens. It is known that antibodies recognize the unique conformations and spatial locations on the surface of antigens. Therefore, epitopes are defined as the portions of the antigen molecules, which are responsible for specificity of the antigens in Ag-Ab reactions and that interact with the antigen binding site of antibody (paratope) to which they are complementary.

Types of Epitopes

Both humoral and cellular arms of immune system recognise and react with only specific regions of the pathogen, called epitopes. It has been known that B and T cells recognize different epitopes on the same antigenic molecule.  Thus, there are two types of epitopes, B cell epitope and Th cell epitope.  The B cell epitopes are accessible, hydrophilic regions and majority of them are capable of neutralisation.  Antibodies produced by B cells recognise the intact antigen in its native conformation.  The epitopes recognized by T cells are products of processed or partially degraded proteins that are bound to MHC molecules and are usually amphipathic (i.e., alternating hydrophobic and hydrophilic) regions.
The B cell epitopes can be contiguous / Sequential (when Ab binds to a contiguous stretch of amino acid residues that are linked by peptide bond) or non-contiguous / Conformational (when Ab binds to non-contiguous residues, brought together by folding of polypeptide chain).  The specificity of sequential epitopes (SE) is determined by the sequence of subunits (e.g. amino acids). On the other hand, specificity of conformational epitopes (CE) depends on the spatial folding or conformation of the contributing individual sequential epitopes.

Existing Approaches to predict B-cell epitopes

Sequential epitopes

Conformational epitopes

CE Algorithm

Accuracy of Algorithm

CE predicts the Conformational Epitopes with an accuracy of 75%, when tested using 21 X-ray diffracted co-crystal structure complexes of antigen and antibodies that are available in PDB database (unpublished).

Software details

Scripting language: CGI Perl
Accessibility calculation: Voronoi procedure implemented by McConkey et al (2002).
Server : Apache on Linux 9.2

System requirements
IE4+ and Netscape 4 and above.

How to Calculate CE
Click on upload button to start calculation. Once the message "Processing Completed" appears, results can be accessible for both sequential epitopes and conformational epitopes using hyperlinks .

CE Home Page

Input files 

User has to upload 3D coordinate file in PDB format
Sample input file

Output file
CE lists both, Conformational and Sequential epitopes. Results are saved as html file.
Sample output file


Algorithm development

Urmila Kulkarni- Kale & A. S. Kolaskar

Server implementation
Shriram Bhosle


Sunita Manjari

Contact Details
Prof. A. S. Kolaskar                 Dr.Urmila Kulkarni-Kale
Former Vice-Chancellor,          Information Scientist
University of Pune                   Bioinformatics Centre
Pune 411 007                           University of Pune, Pune 411 007

Phone:     +91 20 2569 0195/2569 2039

Fax:        +91 20 2569 0087