Campus Units
Genetics, Development and Cell Biology, Bioinformatics and Computational Biology, Computer Science
Document Type
Article
Publication Version
Accepted Manuscript
Publication Date
2008
Journal or Book Title
Journal of Molecular Recognition
Volume
21
Issue
4
First Page
243
Last Page
255
DOI
10.1002/jmr.893
Abstract
The identification and characterization of B-cell epitopes play an important role in vaccine design, immunodiagnostic tests, and antibody production. Therefore, computational tools for reliably predicting linear B-cell epitopes are highly desirable. We evaluated Support Vector Machine (SVM) classifiers trained utilizing five different kernel methods using fivefold cross-validation on a homology-reduced data set of 701 linear B-cell epitopes, extracted from Bcipep database, and 701 non-epitopes, randomly extracted from SwissProt sequences. Based on the results of our computational experiments, we propose BCPred, a novel method for predicting linear B-cell epitopes using the subsequence kernel. We show that the predictive performance of BCPred (AUC = 0.758) outperforms 11 SVM-based classifiers developed and evaluated in our experiments as well as our implementation of AAP (AUC = 0.7), a recently proposed method for predicting linear B-cell epitopes using amino acid pair antigenicity. Furthermore, we compared BCPred with AAP and ABCPred, a method that uses recurrent neural networks, using two data sets of unique B-cell epitopes that had been previously used to evaluate ABCPred. Analysis of the data sets used and the results of this comparison show that conclusions about the relative performance of different B-cell epitope prediction methods drawn on the basis of experiments using data sets of unique B-cell epitopes are likely to yield overly optimistic estimates of performance of evaluated methods. This argues for the use of carefully homology-reduced data sets in comparing B-cell epitope prediction methods to avoid misleading conclusions about how different methods compare to each other. Our homologyreduced data set and implementations of BCPred as well as the APP method are publicly available through our web-based server, BCPREDS, at: http://ailab.cs.iastate.edu/bcpreds/.
Copyright Owner
John Wiley & Sons, Ltd.
Copyright Date
2008
Language
en
File Format
application/pdf
Recommended Citation
EL-Manzalawy, Yasser; Dobbs, Drena; and Honavar, Vasant, "Predicting linear B-cell epitopes using string kernels" (2008). Genetics, Development and Cell Biology Publications. 114.
https://lib.dr.iastate.edu/gdcb_las_pubs/114
Included in
Bioinformatics Commons, Cell and Developmental Biology Commons, Computational Biology Commons
Comments
This is the peer reviewed version of the following article: EL-Manzalawy, Y., Dobbs, D. and Honavar, V. (2008), Predicting linear B-cell epitopes using string kernels. J. Mol. Recognit., 21: 243–255 , which has been published in final form at doi: 10.1002/jmr.893. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.