Benchmarking B cell epitope prediction: underperformance of existing methods.

by: MJ Blythe, DR Flower

Protein Sci, Vol. 14, No. 1. (January 2005), pp. 246-248.

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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.

@article{citeulike:1606856, 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.}, address = {Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK. martin.blythe@jenner.ac.uk}, author = {Blythe, M. J. and Flower, D. R. }, citeulike-article-id = {1606856}, doi = {http://dx.doi.org/10.1110/ps.041059505}, issn = {0961-8368}, journal = {Protein Sci}, month = {January}, number = {1}, pages = {246--248}, posted-at = {2007-08-30 09:28:17}, priority = {0}, title = {Benchmarking B cell epitope prediction: underperformance of existing methods.}, url = {http://dx.doi.org/10.1110/ps.041059505}, volume = {14}, year = {2005} }

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TY - JOUR ID - citeulike:1606856 L3 - citeulike-article-id:1606856 TI - Benchmarking B cell epitope prediction: underperformance of existing methods. JF - Protein Sci VL - 14 IS - 1 SP - 246 EP - 248 AD - Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG20 7NN, UK. martin.blythe@jenner.ac.uk SN - 0961-8368 N2 - 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. AU - Blythe, MJ AU - Flower, DR PY - 2005/01// UR - http://dx.doi.org/10.1110/ps.041059505 ER -

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