Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods

PLoS One. 2013 Apr 19;8(4):e62249. doi: 10.1371/journal.pone.0062249. Print 2013.


Accurate prediction of B-cell antigenic epitopes is important for immunologic research and medical applications, but compared with other bioinformatic problems, antigenic epitope prediction is more challenging because of the extreme variability of antigenic epitopes, where the paratope on the antibody binds specifically to a given epitope with high precision. In spite of the continuing efforts in the past decade, the problem remains unsolved and therefore still attracts a lot of attention from bioinformaticists. Recently, several discontinuous epitope prediction servers became available, and it is intriguing to review all existing methods and evaluate their performances on the same benchmark. In addition, these methods are also compared against common binding site prediction algorithms, since they have been frequently used as substitutes in the absence of good epitope prediction methods.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Antigens / chemistry*
  • Area Under Curve
  • Binding Sites / immunology
  • Computational Biology / methods*
  • Databases, Protein
  • Epitopes, B-Lymphocyte / chemistry*
  • Humans
  • Protein Binding / immunology
  • Protein Conformation


  • Antigens
  • Epitopes, B-Lymphocyte

Grant support

This project was supported by University of Nebraska – Lincoln start-up funds (to CZ). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.