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Benchmarking B cell epitope prediction: Underperformance of existing methods
Author(s) -
Blythe Martin J.,
Flower Darren R.
Publication year - 2005
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.041059505
Subject(s) - epitope , computational biology , linear epitope , polyclonal antibodies , benchmarking , computer science , biology , genetics , antibody , marketing , business
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.