Dec 6, 2008

ElliPro: a new structure-based tool for the prediction of antibody epitopes

BMC Bioinformatics
Julia PonomarenkoBjoern Peters

Abstract

Reliable prediction of antibody, or B-cell, epitopes remains challenging yet highly desirable for the design of vaccines and immunodiagnostics. A correlation between antigenicity, solvent accessibility, and flexibility in proteins was demonstrated. Subsequently, Thornton and colleagues proposed a method for identifying continuous epitopes in the protein regions protruding from the protein's globular surface. The aim of this work was to implement that method as a web-tool and evaluate its performance on discontinuous epitopes known from the structures of antibody-protein complexes. Here we present ElliPro, a web-tool that implements Thornton's method and, together with a residue clustering algorithm, the MODELLER program and the Jmol viewer, allows the prediction and visualization of antibody epitopes in a given protein sequence or structure. ElliPro has been tested on a benchmark dataset of discontinuous epitopes inferred from 3D structures of antibody-protein complexes. In comparison with six other structure-based methods that can be used for epitope prediction, ElliPro performed the best and gave an AUC value of 0.732, when the most significant prediction was considered for each protein. Since the rank of the best prediction ...Continue Reading

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  • Citations155

References

Mentioned in this Paper

Protrusion
Twitter Messaging
Binding Sites, Antibody
Vaccines
Complex (molecular entity)
Lysozyme Test
Plasmodium vivax
FN1 wt Allele
Docking -molecular Interaction
Computer Programs and Programming

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