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Protein Sci. 2005 Jan;14(1):246-8. Epub 2004 Dec 2.

Benchmarking B cell epitope prediction: underperformance of existing methods.

Author information

1
Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK. martin.blythe@jenner.ac.uk

Abstract

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 10(6) 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.

PMID:
15576553
PMCID:
PMC2253337
DOI:
10.1110/ps.041059505
[Indexed for MEDLINE]
Free PMC Article

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