Prediction of residues in discontinuous B-cell epitopes using protein 3D structures

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Prediction of residues in discontinuous B-cell epitopes using protein 3D structures

Authors
Publisher
Wiley-Blackwell Publishing, Inc.
Keywords
  • Here
  • Spatial Information
  • Discovery Of Discontinuous B-Cell Epitopes Is A Major Challenge In Vaccine Design
  • Previous Epitope Prediction Methods Have Mostly Been Based On Protein Sequences And Are Not Very Eff
  • We Present Discotope
  • A Novel Method For Discontinuous Epitope Prediction That Uses Protein Three-Dimensional Structural D
  • The Method Is Based On Amino Acid Statistics
  • And Surface Accessibility In A Compiled Data Set Of Discontinuous Epitopes Determined By X-Ray Cryst
  • Discotope Is The First Method To Focus Explicitly On Discontinuous Epitopes
  • We Show That The New Structure-Based Method Has A Better Performance For Predicting Residues Of Disc
  • And That It Can Successfully Predict Epitope Residues That Have Been Identified By Different Techniq
  • Discotope Detects 15
  • 5% Of Residues Located In Discontinuous Epitopes With A Specificity Of 95%
  • At This Level Of Specificity
  • The Conventional Parker Hydrophilicity Scale For Predicting Linear B-Cell Epitopes Identifies Only 1
  • 0% Of Residues Located In Discontinuous Epitopes
  • Predictions By The Discotope Method Can Guide Experimental Epitope Mapping In Both Rational Vaccine
  • And May Lead To More Efficient Epitope Identification

Abstract

Prediction of residues in discontinuous B-cell epitopes using protein 3D structures - DTU Orbit (28/02/14) Prediction of residues in discontinuous B-cell epitopes using protein 3D structures - DTU Orbit (28/02/14) Prediction of residues in discontinuous B-cell epitopes using protein 3D structures Discovery of discontinuous B-cell epitopes is a major challenge in vaccine design. Previous epitope prediction methods have mostly been based on protein sequences and are not very effective. Here, we present DiscoTope, a novel method for discontinuous epitope prediction that uses protein three-dimensional structural data. The method is based on amino acid statistics, spatial information, and surface accessibility in a compiled data set of discontinuous epitopes determined by X-ray crystallography of antibody/antigen protein complexes. DiscoTope is the first method to focus explicitly on discontinuous epitopes. We show that the new structure-based method has a better performance for predicting residues of discontinuous epitopes than methods based solely on sequence information, and that it can successfully predict epitope residues that have been identified by different techniques. DiscoTope detects 15.5% of residues located in discontinuous epitopes with a specificity of 95%. At this level of specificity, the conventional Parker hydrophilicity scale for predicting linear B-cell epitopes identifies only 11.0% of residues located in discontinuous epitopes. Predictions by the DiscoTope method can guide experimental epitope mapping in both rational vaccine design and development of diagnostic tools, and may lead to more efficient epitope identification. General information State: Published Organisations: Center for Biological Sequence Analysis, Department of Systems Biology Authors: Andersen, P. (Ekstern), Nielsen, M. (Intern), Lund, O. (Intern) Keywords: (vaccine design, hydrophilicity, antibody, protein structure, antigen, B-cell epitope, discontinuous epitopes, accessibility) Pages: 2558-2567 Pub

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