Benchmarking B cell epitope prediction: underperformance of existing methods

Martin J. Blythe, Darren R. Flower

Research output: Contribution to journalArticlepeer-review


Sequence profiling is used routinely to predict the location of B-cell epitopes. In the postgenomic era, the need for reliable epitope prediction is clear. We assessed 484 amino acid propensity scales in combination with ranges of plotting parameters to examine exhaustively the correlation of peaks and epitope location within 50 proteins mapped for polyclonal responses. After examining more than 106 combinations, we found that even the best set of scales and parameters performed only marginally better than random. Our results confirm the null hypothesis: Single-scale amino acid propensity profiles cannot be used to predict epitope location reliably. The implication for studies using such methods is obvious.
Original languageEnglish
Pages (from-to)246-248
Number of pages3
JournalProtein Science
Issue number1
Publication statusPublished - Jan 2005


  • active site/binding site/epitope mapping
  • proteins of the immune system
  • immunological methods
  • epitope prediction


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