Recent advances in B-cell epitope prediction methods

Identification of epitopes that invoke strong responses from B-cells is one of the key steps in designing effective vaccines against pathogens. Because experimental determination of epitopes is expensive in terms of cost, time, and effort involved, there is an urgent need for computational methods for reliable identification of B-cell epitopes. Although several computational tools for predicting B-cell epitopes have become available in recent years, the predictive performance of existing tools remains far from ideal. We review recent advances in computational methods for B-cell epitope prediction, identify some gaps in the current state of the art, and outline some promising directions for improving the reliability of such methods.

[1]  M. Levitt.  A simplified representation of protein conformations for rapid simulation of protein folding. , 1976, Journal of molecular biology.

[2]  Anna Tramontano,et al.  The MEPS server for identifying protein conformational epitopes , 2007, BMC Bioinformatics.

[3]  Ruth Nussinov,et al.  SiteLight: Binding‐site prediction using phage display libraries , 2003, Protein science : a publication of the Protein Society.

[4]  O. Lund,et al.  Prediction of residues in discontinuous B‐cell epitopes using protein 3D structures , 2006, Protein science : a publication of the Protein Society.

[5]  A. Giuliani,et al.  A computational approach identifies two regions of Hepatitis C Virus E1 protein as interacting domains involved in viral fusion process , 2009, BMC Structural Biology.

[6]  G. Schneider,et al.  PocketPicker: analysis of ligand binding-sites with shape descriptors , 2007, Chemistry Central Journal.

[7]  Morten Nielsen,et al.  Improved method for predicting linear B-cell epitopes , 2006, Immunome research.

[8]  K. R. Woods,et al.  Prediction of protein antigenic determinants from amino acid sequences. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[9]  A Sette,et al.  Meta‐analysis of immune epitope data for all Plasmodia: overview and applications for malarial immunobiology and vaccine‐related issues , 2009, Parasite immunology.

[10]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence data bank and its supplement TrEMBL , 1997, Nucleic Acids Res..

[11]  Vasant G Honavar,et al.  Prediction of RNA binding sites in proteins from amino acid sequence. , 2006, RNA.

[12]  Ian Witten,et al.  Data Mining , 2000 .

[13]  Bernd Mayer,et al.  Machine learning approaches for prediction of linear B‐cell epitopes on proteins , 2006, Journal of molecular recognition : JMR.

[14]  T. Hamelryck.  An amino acid has two sides: A new 2D measure provides a different view of solvent exposure , 2005, Proteins.

[15]  G. Walter,et al.  Production and use of antibodies against synthetic peptides. , 1986, Journal of immunological methods.

[16]  David R. Westhead,et al.  Improved prediction of protein-protein binding sites using a support vector machines approach. , 2005, Bioinformatics.

[17]  Urmila Kulkarni-Kale,et al.  CEP: a conformational epitope prediction server , 2005, Nucleic Acids Res..

[18]  A Tramontano,et al.  Mapping epitopes on protein surfaces. , 1995, Biopolymers.

[19]  Chao Zhang,et al.  FastContact: rapid estimate of contact and binding free energies , 2005, Bioinform..

[20]  Arno Lukas,et al.  Analysis and prediction of protective continuous B-cell epitopes on pathogen proteins , 2008, Immunome research.

[21]  Sandor Vajda,et al.  ClusPro: an automated docking and discrimination method for the prediction of protein complexes , 2004, Bioinform..

[22]  Solène Grosdidier,et al.  Identification of hot-spot residues in protein-protein interactions by computational docking , 2008, BMC Bioinformatics.

[23]  Vasant Honavar,et al.  Predicting flexible length linear B-cell epitopes. , 2008, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

[24]  M Ouali,et al.  Cascaded multiple classifiers for secondary structure prediction , 2000, Protein science : a publication of the Protein Society.

[25]  Ian H. Witten,et al.  Data mining: practical machine learning tools and techniques, 3rd Edition , 1999 .

[26]  Bjoern Peters,et al.  Analysis of epitope information related to Bacillus anthracis and Clostridium botulinum , 2008, Expert review of vaccines.

[27]  M. V. Van Regenmortel,et al.  What is a B-cell epitope? , 2009, Methods in molecular biology.

[28]  Violaine Moreau,et al.  Discontinuous epitope prediction based on mimotope analysis , 2006, Bioinform..

[29]  Mike Schutkowski,et al.  Epitope mapping protocols. Preface. , 2009, Methods in molecular biology.

[30]  M. V. Regenmortel,et al.  What is a B-cell epitope? , 2009 .

[31]  Peixiang Cai,et al.  Predicting protein structural class with pseudo-amino acid composition and support vector machine fusion network. , 2006, Analytical biochemistry.

[32]  Vasant Honavar,et al.  Predicting DNA-binding sites of proteins from amino acid sequence , 2006, BMC Bioinformatics.

[33]  Arno Lukas,et al.  Identification of discontinuous antigenic determinants on proteins based on shape complementarities , 2007, Journal of molecular recognition : JMR.

[34]  P. Karplus,et al.  Prediction of chain flexibility in proteins , 1985, Naturwissenschaften.

[35]  Vasant Honavar,et al.  Glycosylation site prediction using ensembles of Support Vector Machine classifiers , 2007, BMC Bioinformatics.

[36]  K. Chou,et al.  Prediction of linear B-cell epitopes using amino acid pair antigenicity scale , 2007, Amino Acids.

[37]  Bjoern Peters,et al.  An analysis of the epitope knowledge related to Mycobacteria , 2007, Immunome research.

[38]  Nimrod D. Rubinstein,et al.  Computational characterization of B-cell epitopes. , 2008, Molecular immunology.

[39]  David J. Hand,et al.  Measuring classifier performance: a coherent alternative to the area under the ROC curve , 2009, Machine Learning.

[40]  Nello Cristianini,et al.  Classification using String Kernels , 2000 .

[41]  R. Raz,et al.  ProMate: a structure based prediction program to identify the location of protein-protein binding sites. , 2004, Journal of molecular biology.

[42]  Pierre Baldi,et al.  PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure , 2008, Bioinform..

[43]  W R Taylor,et al.  Location of ‘continuous’ antigenic determinants in the protruding regions of proteins. , 1986, The EMBO journal.

[44]  Avner Schlessinger,et al.  Towards a consensus on datasets and evaluation metrics for developing B‐cell epitope prediction tools , 2007, Journal of molecular recognition : JMR.

[45]  Scott Dick,et al.  Classifier ensembles for protein structural class prediction with varying homology. , 2006, Biochemical and biophysical research communications.

[46]  S. Jones,et al.  Prediction of protein-protein interaction sites using patch analysis. , 1997, Journal of molecular biology.

[47]  Roded Sharan,et al.  Pepitope: epitope mapping from affinity-selected peptides , 2007, Bioinform..

[48]  Itay Mayrose,et al.  Stepwise prediction of conformational discontinuous B‐cell epitopes using the Mapitope algorithm , 2007, Proteins.

[49]  E Westhof,et al.  Correlation between the location of antigenic sites and the prediction of turns in proteins. , 1993, Immunology letters.

[50]  Jan M. Kriegl,et al.  PocketGraph: graph representation of binding site volumes , 2009 .

[51]  Johannes Söllner,et al.  Selection and combination of machine learning classifiers for prediction of linear B‐cell epitopes on proteins , 2006, Journal of molecular recognition : JMR.

[52]  Sudipto Saha,et al.  Prediction of continuous B‐cell epitopes in an antigen using recurrent neural network , 2006, Proteins.

[53]  Itay Mayrose,et al.  ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures , 2005, Nucleic Acids Res..

[54]  J Ignacio Casal,et al.  Characterisation of a protective linear B cell epitope against feline parvoviruses. , 2001, Vaccine.

[55]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[56]  Darren R. Flower,et al.  Bioinformatics for Vaccinology , 2008 .

[57]  Xiuzhen Zhang,et al.  Large-scale prediction of long disordered regions in proteins using random forests , 2009, BMC Bioinformatics.

[58]  Xiao Sun,et al.  Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature , 2008, Bioinform..

[59]  Nimrod D. Rubinstein,et al.  Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm , 2006, Nucleic acids research.

[60]  Pierre Baldi,et al.  Assessing the accuracy of prediction algorithms for classification: an overview , 2000, Bioinform..

[61]  Ruth Nussinov,et al.  PatchDock and SymmDock: servers for rigid and symmetric docking , 2005, Nucleic Acids Res..

[62]  Gajendra P. S. Raghava,et al.  BcePred: Prediction of Continuous B-Cell Epitopes in Antigenic Sequences Using Physico-chemical Properties , 2004, ICARIS.

[63]  Vasant Honavar,et al.  A two-stage classifier for identification of protein-protein interface residues , 2004, ISMB/ECCB.

[64]  L. T. Ten Eyck,et al.  Rapid atomic density methods for molecular shape characterization. , 2001, Journal of molecular graphics & modelling.

[65]  Pierre Baldi,et al.  COBEpro: a novel system for predicting continuous B-cell epitopes. , 2009, Protein engineering, design & selection : PEDS.

[66]  Ruben Abagyan,et al.  PIER: Protein interface recognition for structural proteomics , 2007, Proteins.

[67]  J Snoeys,et al.  The impact of antigen expression in antigen-presenting cells on humoral immune responses against the transgene product , 2010, Gene Therapy.

[68]  M. Gajhede,et al.  Dominant Epitopes and Allergic Cross-Reactivity: Complex Formation Between a Fab Fragment of a Monoclonal Murine IgG Antibody and the Major Allergen from Birch Pollen Bet v 11 , 2000, The Journal of Immunology.

[69]  Vasant G Honavar,et al.  Predicting linear B‐cell epitopes using string kernels , 2008, Journal of molecular recognition : JMR.

[70]  Sandor Vajda,et al.  CAPRI: A Critical Assessment of PRedicted Interactions , 2003, Proteins.

[71]  J. Skehel,et al.  Structural evidence for recognition of a single epitope by two distinct antibodies , 2000, Proteins.

[72]  Jean-Luc Pellequer,et al.  BEPITOPE: predicting the location of continuous epitopes and patterns in proteins , 2003, Journal of molecular recognition : JMR.

[73]  A. Alix,et al.  Predictive estimation of protein linear epitopes by using the program PEOPLE. , 1999, Vaccine.

[74]  Karina Yusim,et al.  Immunoinformatics Comes of Age , 2006, PLoS Comput. Biol..

[75]  Boqin Qiang,et al.  Improving the prediction of human microRNA target genes by using ensemble algorithm , 2007, FEBS letters.

[76]  Wei Li,et al.  ElliPro: a new structure-based tool for the prediction of antibody epitopes , 2008, BMC Bioinformatics.

[77]  John Moult,et al.  A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. , 2005, Current opinion in structural biology.

[78]  Costas S. Iliopoulos,et al.  An algorithm for mapping short reads to a dynamically changing genomic sequence , 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

[79]  D. Flower,et al.  Benchmarking B cell epitope prediction: Underperformance of existing methods , 2005, Protein science : a publication of the Protein Society.

[80]  Darren R Flower.  Immunoinformatics. Predicting immunogenicity in silico. Preface. , 2007, Methods in molecular biology.

[81]  R. Hodges,et al.  New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. , 1986, Biochemistry.

[82]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[83]  Qing Zhang,et al.  Immune epitope database analysis resource (IEDB-AR) , 2008, Nucleic Acids Res..

[84]  J. Thornton,et al.  Continuous and discontinuous protein antigenic determinants , 1986, Nature.

[85]  E. Emini,et al.  Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide , 1985, Journal of virology.

[86]  E. Davidson,et al.  IMMUNOINFORMATICS: PREDICTING IMMUNOGENICITY IN SILICO , 2008 .

[87]  Steve Wilson,et al.  The Immune Epitope Database and Analysis Resource: From Vision to Blueprint , 2005, PLoS biology.

[88]  E Westhof,et al.  Predicting location of continuous epitopes in proteins from their primary structures. , 1991, Methods in enzymology.

[89]  Gajendra P.S. Raghava,et al.  Prediction of RNA binding sites in a protein using SVM and PSSM profile , 2008, Proteins.

[90]  L. T. Ten Eyck,et al.  Protein docking using continuum electrostatics and geometric fit. , 2001, Protein engineering.

[91]  Vasant Honavar,et al.  Predicting Protective Linear B-Cell Epitopes Using Evolutionary Information , 2008, 2008 IEEE International Conference on Bioinformatics and Biomedicine.