Pepitope: epitope mapping from affinity-selected peptides

• Published in: Bioinformatics Vol. 23; no. 23; pp. 3244 - 3246
• Main Authors: 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
• Format: Journal Article Web Resource
• Language: English
• Published: Oxford Oxford University Press 01.12.2007; Oxford Publishing Limited (England)
• Subjects: Algorithms; Amino Acid Sequence; Applications Notes; Binding Sites; Biological and medical sciences; Epitope Mapping - methods; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Molecular Sequence Data; Peptides - chemistry; Peptides - immunology; Protein Binding; Sequence Alignment - methods; Sequence Analysis, Protein - methods; Software; Antigenic determinant; Peptides; Bioinformatics
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btm493

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@post.tau.ac.il