Predicting protective linear B-cell epitopes using evolutionary information

Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar

Research output: Chapter in Book/Report/Conference proceedingConference contribution

10 Citations (Scopus)

Abstract

Mapping B-cell epitopes plays an important role in vaccine design, immunodiagnostic tests, and antibody production. Because the experimental determination of B-cell epitopes is time-consuming and expensive, there is an urgent need for computational methods for reliable identification of putative B-cell epitopes from antigenic sequences. In this study, we explore the utility of evolutionary profiles derived from antigenic sequences in improving the performance of machine learning methods for protective linear B-cell epitope prediction. Specifically, we compare propensity scale based methods with a Naive Bayes classifier using three different representations of the classifier input: amino acid identities, position specific scoring matrix (PSSM) profiles, and dipeptide composition. We find that in predicting protective linear B-cell epitopes, a Naive Bayes classifier trained using PSSM profiles significantly outperforms the propensity scale based methods as well as the Naive Bayes classifiers trained using the amino acid identity or dipeptide composition representations of input data.

Original languageEnglish (US)
Title of host publicationProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
Pages289-292
Number of pages4
DOIs
StatePublished - Dec 1 2008
Event2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 - Philadelphia, PA, United States
Duration: Nov 3 2008Nov 5 2008

Publication series

NameProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008

Other

Other2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
CountryUnited States
CityPhiladelphia, PA
Period11/3/0811/5/08

Fingerprint

B-Lymphocyte Epitopes
Epitopes
Cells
Classifiers
Position-Specific Scoring Matrices
Dipeptides
Amino acids
Amino Acids
Vaccines
Computational methods
Chemical analysis
Antibodies
Antibody Formation
Learning systems

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Information Systems
  • Biomedical Engineering

Cite this

El-Manzalawy, Y., Dobbs, D., & Honavar, V. (2008). Predicting protective linear B-cell epitopes using evolutionary information. In Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 (pp. 289-292). [4684905] (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008). https://doi.org/10.1109/BIBM.2008.80
El-Manzalawy, Yasser ; Dobbs, Drena ; Honavar, Vasant. / Predicting protective linear B-cell epitopes using evolutionary information. Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. 2008. pp. 289-292 (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008).
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El-Manzalawy, Y, Dobbs, D & Honavar, V 2008, Predicting protective linear B-cell epitopes using evolutionary information. in Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008., 4684905, Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008, pp. 289-292, 2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008, Philadelphia, PA, United States, 11/3/08. https://doi.org/10.1109/BIBM.2008.80

Predicting protective linear B-cell epitopes using evolutionary information. / El-Manzalawy, Yasser; Dobbs, Drena; Honavar, Vasant.

Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. 2008. p. 289-292 4684905 (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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El-Manzalawy Y, Dobbs D, Honavar V. Predicting protective linear B-cell epitopes using evolutionary information. In Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. 2008. p. 289-292. 4684905. (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008). https://doi.org/10.1109/BIBM.2008.80