Abstract
This work deals with the use of predictors to identify useful B-cell linear epitopes to develop immunoassays. Experimental techniques to meet this goal are quite expensive and time consuming. Therefore, we tested 5 free, online prediction methods (AAPPred, ABCpred, BcePred, BepiPred and Antigenic) widely used for predicting linear epitopes, using the primary structure of the protein as the only input. We chose a set of 65 experimentally well documented epitopes obtained by the most reliable experimental techniques as our true positive set. To compare the quality of the predictor methods we used their positive predictive value (PPV), i.e. the proportion of the predicted epitopes that are true, experimentally confirmed epitopes, in relation to all the epitopes predicted. We conclude that AAPPred and ABCpred yield the best results as compared with the other programs and with a random prediction procedure. Our results also indicate that considering the consensual epitopes predicted by several programs does not improve the PPV.
Keywords: Diagnostic, epitope, immunochemical, linear B-cell epitopes, prediction, program, reagents.
Protein & Peptide Letters
Title:Evaluation and Comparison of the Ability of Online Available Prediction Programs to Predict True Linear B-cell Epitopes
Volume: 20 Issue: 6
Author(s): Juan G. Costa, Pablo L. Faccendini, Silvano J. Sferco, Claudia M. Lagier and Ivan S. Marcipar
Affiliation:
Keywords: Diagnostic, epitope, immunochemical, linear B-cell epitopes, prediction, program, reagents.
Abstract: This work deals with the use of predictors to identify useful B-cell linear epitopes to develop immunoassays. Experimental techniques to meet this goal are quite expensive and time consuming. Therefore, we tested 5 free, online prediction methods (AAPPred, ABCpred, BcePred, BepiPred and Antigenic) widely used for predicting linear epitopes, using the primary structure of the protein as the only input. We chose a set of 65 experimentally well documented epitopes obtained by the most reliable experimental techniques as our true positive set. To compare the quality of the predictor methods we used their positive predictive value (PPV), i.e. the proportion of the predicted epitopes that are true, experimentally confirmed epitopes, in relation to all the epitopes predicted. We conclude that AAPPred and ABCpred yield the best results as compared with the other programs and with a random prediction procedure. Our results also indicate that considering the consensual epitopes predicted by several programs does not improve the PPV.
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Cite this article as:
Costa Juan G., Faccendini Pablo L., Sferco Silvano J., Lagier Claudia M. and Marcipar Ivan S., Evaluation and Comparison of the Ability of Online Available Prediction Programs to Predict True Linear B-cell Epitopes, Protein & Peptide Letters 2013; 20 (6) . https://dx.doi.org/10.2174/0929866511320060011
DOI https://dx.doi.org/10.2174/0929866511320060011 |
Print ISSN 0929-8665 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5305 |
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