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Bioinformatics Advance Access originally published online on October 31, 2007
Bioinformatics 2007 23(23):3244-3246; doi:10.1093/bioinformatics/btm493
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Pepitope: epitope mapping from affinity-selected peptides

Itay Mayrose 1, Osnat Penn 1, Elana Erez 1, Nimrod D. Rubinstein 1, Tomer Shlomi 2, Natalia Tarnovitski Freund 1, Erez M. Bublil 1, Eytan Ruppin 2, Roded Sharan 2, Jonathan M. Gershoni 1, Eric Martz 3 and Tal Pupko 1,*

1Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, 2School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel and 3Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA

*To whom correspondence should be addressed.


  Abstract

Identifying the epitope to which an antibody binds is central for many immunological applications such as drug design and vaccine development. The Pepitope server is a web-based tool that aims at predicting discontinuous epitopes based on a set of peptides that were affinity-selected against a monoclonal antibody of interest. The server implements three different algorithms for epitope mapping: PepSurf, Mapitope, and a combination of the two. The rationale behind these algorithms is that the set of peptides mimics the genuine epitope in terms of physicochemical properties and spatial organization. When the three-dimensional (3D) structure of the antigen is known, the information in these peptides can be used to computationally infer the corresponding epitope. A user-friendly web interface and a graphical tool that allows viewing the predicted epitopes were developed. Pepitope can also be applied for inferring other types of protein–protein interactions beyond the immunological context, and as a general tool for aligning linear sequences to a 3D structure.

Availability: http://pepitope.tau.ac.il/

Contact: talp{at}post.tau.ac.il

Associate Editor: Alfonso Valencia

Received on August 12, 2007; revised on September 25, 2007; accepted on September 26, 2007

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