Skip to main content

In Silico Models for B-Cell Epitope Recognition and Signaling

  • Protocol
  • First Online:
Book cover In Silico Models for Drug Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 993))

Abstract

Tremendous technological advances in peptide synthesis and modification in recent years have resolved the major limitations of peptide-based vaccines. B-cell epitopes are major components of these vaccines (besides having other biological applications). Researchers have been developing in silico or computational models for the prediction of both linear and conformational B-cell epitopes, enabling immunologists and clinicians to identify the most promising epitopes for characterization in the laboratory. Attempts are also ongoing in systems biology to delineate the signaling networks in immune cells. Here we present all possible in silico models developed thus far in these areas.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Croft NP, Purcell AW (2011) Peptidomimetics: modifying peptides in the pursuit of better vaccines. Expert Rev Vaccines 10:211–226

    Article  CAS  PubMed  Google Scholar 

  2. Dudek NL, Perlmutter P, Aguilar MI et al (2010) Epitope discovery and their use in peptide based vaccines. Curr Pharm Des 16:3149–3157

    Article  CAS  PubMed  Google Scholar 

  3. Purcell AW, McCluskey J, Rossjohn J (2007) More than one reason to rethink the use of peptides in vaccine design. Nat Rev Drug Discov 6:404–414

    Article  CAS  PubMed  Google Scholar 

  4. Bryson CJ, Jones TD, Baker MP (2010) Prediction of immunogenicity of therapeutic proteins: validity of computational tools. BioDrugs 24:1–8

    Article  CAS  PubMed  Google Scholar 

  5. Steere AC, Drouin EE, Glickstein LJ (2011) Relationship between immunity to Borrelia burgdorferi outer-surface protein A (OspA) and Lyme arthritis. Clin Infect Dis 52(Suppl 3):s259–s265

    Article  CAS  PubMed  Google Scholar 

  6. Gershoni JM, Roitburd-Berman A, Siman-Tov DD et al (2007) Epitope mapping: the first step in developing epitope-based vaccines. BioDrugs 21:145–156

    Article  CAS  PubMed  Google Scholar 

  7. Tomar N, De RK (2010) Immunoinformatics: an integrated scenario. Immunology 131:153–168

    Article  CAS  PubMed  Google Scholar 

  8. Yang X, Yu X (2009) An introduction to epitope prediction methods and software. Rev Med Virol 19:77–96

    Article  CAS  PubMed  Google Scholar 

  9. Hopp TP, Woods KR (1981) Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci USA 78:3824–3828

    Article  CAS  PubMed  Google Scholar 

  10. Chou PY, Fasman GD (1974) Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry 13:211–222

    Article  CAS  PubMed  Google Scholar 

  11. Levitt M (1976) A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 104:59–107

    Article  CAS  PubMed  Google Scholar 

  12. Parker JM, Guo D, Hodges RS (1986) 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. Biochemistry 25:5425–5432

    Article  CAS  PubMed  Google Scholar 

  13. Emini EA, Hughes JV, Perlow DS, Boger J (1985) Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol 55:836–839

    CAS  PubMed  Google Scholar 

  14. Karplus PA, Schulz GE (1985) Prediction of chain flexibility in proteins - a tool for the selection of peptide antigens. Naturwissenschaften 72:212–213

    Article  CAS  Google Scholar 

  15. Thornton JM, Edwards MS, Taylor WR, Barlow DJ (1986) Location of ‘continuous’ antigenic determinants in the protruding regions of proteins. EMBO J 5:409–413

    CAS  PubMed  Google Scholar 

  16. Jameson BA, Wolf H (1988) The antigenic index: a novel algorithm for predicting antigenic determinants. Comput Appl Biosci 4:181–186

    CAS  PubMed  Google Scholar 

  17. Pellequer JL, Westhof E, Van Regenmortel MH (1993) Correlation between the location of antigenic sites and the prediction of turns in proteins. Immunol Lett 36:83–99

    Article  CAS  PubMed  Google Scholar 

  18. Pellequer JL, Westhof E (1993) PREDITOP: a program for antigenicity prediction. J Mol Graph 11(204–210):191–202

    Google Scholar 

  19. Alix AJ (1999) Predictive estimation of protein linear epitopes by using the program PEOPLE. Vaccine 18:311–314

    Article  CAS  PubMed  Google Scholar 

  20. Odorico M, Pellequer J (2003) BEPITOPE: predicting the location of continuous epitopes and patterns in proteins. J Mol Recognit 16:20–22

    Article  CAS  PubMed  Google Scholar 

  21. Saha S, Bhasin M, Raghava GP (2005) Bcipep: a database of B-cell epitopes. BMC Genomics 6:79

    Article  PubMed  Google Scholar 

  22. Saha S, Raghava G (2004) BcePred: prediction of continuous B-cell epitopes in antigenic sequences using physico-chemical properties. In: Proceedings of the 3rd international conference on artificial immune systems (ICARUS), 13–16 Sep 2004, Catania, Italy. LNCS 3239: 197–204

    Google Scholar 

  23. Blythe M, Flower D (2005) Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci 14:246–248

    Article  CAS  PubMed  Google Scholar 

  24. Saha S, Raghava G (2006) Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins 65:40–48

    Article  CAS  PubMed  Google Scholar 

  25. Larsen JE, Lund O, Nielsen M (2006) Improved method for predicting linear B-cell epitopes. Immunome Res 2:2

    Article  PubMed  Google Scholar 

  26. Chen J, Liu H, Yang J, Chou KC (2007) Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids 33:423–428

    Article  CAS  PubMed  Google Scholar 

  27. El-Manzalawy Y, Dobbs D, Honavar V (2008) Predicting linear B-cell epitopes using string kernels. J Mol Recognit 21:243–255

    Article  CAS  PubMed  Google Scholar 

  28. Wang HW, Lin YC, Pai TW, Chang HT (2011) Prediction of B-cell linear epitopes with a combination of support vector machine classification and amino acid propensity identification. J Biomed Biotechnol 2011(43):28–30

    Google Scholar 

  29. El-Manzalawy Y, Dobbs D, Honavar V (2008) Predicting flexible length linear B-cell epitopes. Proceedings of the 7th international conference on computational systems bioinformatics, Imperial College Press, London, pp 121–131

    Google Scholar 

  30. Sweredoski M, Baldi P (2009) COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Eng Des Sel 22:113–120

    Article  CAS  PubMed  Google Scholar 

  31. Wee LJ, Simarmata D, Kam YW et al (2010) SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction. BMC Genomics 11(Suppl 4):S21

    Article  PubMed  Google Scholar 

  32. Kulkarni-Kale U, Bhosle S, Kolaskar AS (2005) CEP: a conformational epitope prediction server. Nucleic Acids Res 33:W168–W171

    Article  CAS  PubMed  Google Scholar 

  33. Anderson PH, Nielsen M, Lund O (2006) Prediction of residues in discontinuous B-cell epitopes using protein 3D structure. Protein Sci 15:2558–2567

    Article  Google Scholar 

  34. Ponomarenko JV, Bourne PE (2007) Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol 7:64

    Article  PubMed  Google Scholar 

  35. Rapberger R, Lukas A, Mayer B (2007) Identification of discontinuous antigenic determinants on proteins based on shape complementarities. J Mol Recognit 20:113–121

    Article  CAS  PubMed  Google Scholar 

  36. Ponomarenko J, Bui HH, Li W et al (2008) ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics 9:514

    Article  PubMed  Google Scholar 

  37. Sweredoski M, Baldi P (2008) PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics 24:1459–1460

    Article  CAS  PubMed  Google Scholar 

  38. Rubinstein ND, Mayrose I, Martz E, Pupko T (2009) Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics 10:287

    Article  PubMed  Google Scholar 

  39. Sun J, Wu D, Xu T et al (2009) SEPPA: a computational server for spatial epitope prediction of protein antigens. Nucleic Acids Res 37:W612–W616

    Article  CAS  PubMed  Google Scholar 

  40. Liang S, Zheng D, Standley DM et al (2010) EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC Bioinformatics 11:381

    Article  PubMed  Google Scholar 

  41. Ansari HR, Raghava GP (2010) Identification of conformational B-cell epitopes in an antigen from its primary sequence. Immunome Res 6:6

    Article  PubMed  Google Scholar 

  42. Geysen HM, Rodda SJ, Mason TJ (1986) A priori delineation of a peptide which mimics a discontinuous antigenic determinant. Mol Immunol 23:709–715

    Article  CAS  PubMed  Google Scholar 

  43. Gauld SB, Dal Porto JM, Cambier JC (2002) B cell antigen receptor signaling: roles in cell development and disease. Science 296:1641–1642

    Article  CAS  PubMed  Google Scholar 

  44. Cuesta N, Martin-Cofreces NB, Murga C, van Santen HM (2011) Receptors, signaling networks, and disease. Sci Signal 4:mr3

    Article  PubMed  Google Scholar 

  45. Suresh Babu CV, Joo Song E, Yoo YS (2006) Modeling and simulation in signal transduction pathways: a systems biology approach. Biochimie 88:277–283

    Article  CAS  PubMed  Google Scholar 

  46. Goldstein B, Faeder JR, Hlavacek WS (2004) Mathematical and computational models of immune-receptor signalling. Nat Rev Immunol 4:445–456

    Article  CAS  PubMed  Google Scholar 

  47. Gilman AG, Simon MI, Bourne HR et al (2002) Overview of the alliance for cellular signaling. Nature 420:703–706

    Article  CAS  PubMed  Google Scholar 

  48. Srinivas Reddy A, Tsourkas PK, Raychaudhuri S (2011) Monte Carlo study of B-cell receptor clustering mediated by antigen crosslinking and directed transport. Cell Mol Immunol 8:255–264

    Article  CAS  PubMed  Google Scholar 

  49. Klamt S, Saez-Rodriguez J, Gilles ED (2007) Structural and functional analysis of cellular networks with Cell NetAnalyzer. BMC Syst Biol 1:2

    Article  PubMed  Google Scholar 

  50. Di Cara A, Garg A, De Micheli G et al (2007) Dynamic simulation of regulatory networks using SQUAD. BMC Bioinformatics 8:462

    Article  PubMed  Google Scholar 

  51. Taylor R, Singhal M (2009) Biological network inference and analysis using SEBINI and CABIN. Methods Mol Biol 541:551–576

    Article  CAS  PubMed  Google Scholar 

  52. Liang S, Zheng D, Zhang C, Zacharias M (2009) Prediction of antigenic epitopes on protein surfaces by consensus scoring. BMC Bioinformatics 10:302

    Article  PubMed  Google Scholar 

  53. Moreau V, Fleury C, Piquer D et al (2008) PEPOP: computational design of immunogenic peptides. BMC Bioinformatics 9:71

    Article  PubMed  Google Scholar 

  54. Pacios LF, Tordesillas L, Palacín A et al (2011) LocaPep: localization of epitopes on protein surfaces using peptides from phage display libraries. J Chem Inf Model 51:1465–1473

    Article  CAS  PubMed  Google Scholar 

  55. Chen WH, Sun PP, Lu Y et al (2011) MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries. BMC Bioinformatics 12:199

    Article  PubMed  Google Scholar 

  56. Huang YX, Bao YL, Guo SY et al (2008) Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis. BMC Bioinformatics 9:538

    Article  PubMed  Google Scholar 

  57. Mayrose I, Penn O, Erez E et al (2007) Pepitope: epitope mapping from affinity-selected peptides. Bioinformatics 23:3244–3246

    Article  CAS  PubMed  Google Scholar 

  58. Mayrose I, Shlomi T, Rubinstein ND et al (2007) Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Res 35:69–78

    Article  CAS  PubMed  Google Scholar 

  59. Castrignanò T, De Meo PD, Carrabino D et al (2007) The MEPS server for identifying protein conformational epitopes. BMC Bioinformatics 8:S6

    Article  PubMed  Google Scholar 

  60. Bublil EM, Freund NT, Mayrose I et al (2007) Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins 68:294–304

    Article  CAS  PubMed  Google Scholar 

  61. Moreau V, Granier C, Villard S et al (2006) Discontinuous epitope prediction based on mimotope analysis. Bioinformatics 22:1088–1095

    Article  CAS  PubMed  Google Scholar 

  62. Huang J, Gutteridge A, Honda W, Kanehisa M (2006) MIMOX: a web tool for phage display based epitope mapping. BMC Bioinformatics 7:451

    Article  PubMed  Google Scholar 

  63. Schreiber A, Humbert M, Benz A, Dietrich U (2005) 3D-Epitope-Explorer (3DEX): localization of conformational epitopes within three-dimensional structures of proteins. J Comput Chem 26:879–887

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

H.R.A. is financially supported by the Council of Scientific and Industrial Research (CSIR), New Delhi, India.

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Ansari, H.R., Raghava, G.P.S. (2013). In Silico Models for B-Cell Epitope Recognition and Signaling. In: Kortagere, S. (eds) In Silico Models for Drug Discovery. Methods in Molecular Biology, vol 993. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-342-8_9

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-342-8_9

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-341-1

  • Online ISBN: 978-1-62703-342-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics