Pepitope: epitope mapping from affinity-selected peptides

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

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: