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Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, United Kingdom
(RECEIVED August 20, 2004; FINAL REVISION September 27, 2004; ACCEPTED September 27, 2004)
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.
Keywords: active site/binding site/epitope mapping; proteins of the immune system; immunological methods; epitope prediction
Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041059505.
Reprint requests to: Martin J. Blythe, Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK; e-mail: martin.blythe{at}jenner.ac.uk; fax: +44-1635-577908.
Supplemental material: see www.proteinscience.org
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