Pepitope: epitope mapping from affinity-selected peptides

Bioinformatics. 2007 Dec 1;23(23):3244-6. doi: 10.1093/bioinformatics/btm493. Epub 2007 Oct 31.


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.


Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Binding Sites
  • Epitope Mapping / methods*
  • Molecular Sequence Data
  • Peptides / chemistry*
  • Peptides / immunology*
  • Protein Binding
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*
  • Software*


  • Peptides