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Nucleic Acids Research 2005 33(Web Server Issue):W168-W171; doi:10.1093/nar/gki460
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

CEP: a conformational epitope prediction server

Urmila Kulkarni-Kale*, Shriram Bhosle and A. S. Kolaskar1

Bioinformatics Centre, University of Pune Pune 411 007, India 1Vice-Chancellor's office, University of Pune Pune 411 007, India

*To whom correspondence should be addressed. Tel: +91 20 2569 0195/2569 2039; Fax: +91 20 2569 0087; Email: urmila{at}bioinfo.ernet.in

Received February 14, 2005. Revised April 13, 2005. Accepted April 13, 2005.

CEP server (http://bioinfo.ernet.in/cep.htm) provides a web interface to the conformational epitope prediction algorithm developed in-house. The algorithm, apart from predicting conformational epitopes, also predicts antigenic determinants and sequential epitopes. The epitopes are predicted using 3D structure data of protein antigens, which can be visualized graphically. The algorithm employs structure-based Bioinformatics approach and solvent accessibility of amino acids in an explicit manner. Accuracy of the algorithm was found to be 75% when evaluated using X-ray crystal structures of Ag–Ab complexes available in the PDB. This is the first and the only method available for the prediction of conformational epitopes, which is an attempt to map probable antibody-binding sites of protein antigens.


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