Pepitope: Epitope mapping from affinity-selected peptides

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

115 Scopus citations


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.

Original languageEnglish
Pages (from-to)3244-3246
Number of pages3
Issue number23
StatePublished - Dec 2007


FundersFunder number
Israeli Ministry of Science and Technology
Safra bioinformatics program
Tauber Fund
US National Science Foundation Division of Undergraduate Education
Wolfson Foundation
United States-Israel Binational Science Foundation
Israel Science Foundation


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