Immunoinformatics may lead to a reappraisal of the nature of B cell epitopes and of the feasibility of synthetic peptide vaccines.

[1]  R. Jemmerson,et al.  Antigenicity and native structure of globular proteins: low frequency of peptide reactive antibodies. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Smith Ja,et al.  A proposal for the nomenclature of antigenic sites in peptides and proteins. , 1978 .

[3]  C. Schönbach,et al.  An Update on the Functional Molecular Immunology (FIMM) Database , 2005, Applied bioinformatics.

[4]  M.H.V. Van Regenmortel,et al.  Pitfalls of reductionism in the design of peptide-based vaccines , 2001 .

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

[6]  M. V. Regenmortel,et al.  Structural and functional approaches to the study of protein antigenicity. , 1989, Immunology today.

[7]  L Choulier,et al.  Recognition of peptides by antibodies and investigations of affinity using biosensor technology. , 2001, Combinatorial chemistry & high throughput screening.

[8]  R. Lerner Antibodies of predetermined specificity in biology and medicine. , 1984, Advances in immunology.

[9]  M. V. Regenmortel,et al.  Molecular dissection of protein antigens and the prediction of epitopes , 1988 .

[10]  R L Stanfield,et al.  Antibody-antigen interactions: new structures and new conformational changes. , 1994, Current opinion in structural biology.

[11]  B. Spangler Binding to native proteins by antipeptide monoclonal antibodies. , 1991, Journal of immunology.

[12]  F. Brown,et al.  Intranasal Immunization of Guinea Pigs with an Immunodominant Foot-and-Mouth Disease Virus Peptide Conjugate Induces Mucosal and Humoral Antibodies and Protection against Challenge , 2003, Journal of Virology.

[13]  Bjoern Peters,et al.  An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities , 2005, Immunome research.

[14]  R A Houghten,et al.  Crystal structure of a peptide complex of anti-influenza peptide antibody Fab 26/9. Comparison of two different antibodies bound to the same peptide antigen. , 1994, Journal of molecular biology.

[15]  M. V. Regenmortel,et al.  Mimotopes, continuous paratopes and hydropathic complementarity : Novel approximations in the description of immunochemical specificity , 1998 .

[16]  Neil S. Greenspan,et al.  Defining epitopes: It's not as easy as it seems , 1999, Nature Biotechnology.

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

[18]  H. Bosshard,et al.  Genuine and apparent cross-reaction of polyclonal antibodies to proteins and peptides. , 1994, European journal of biochemistry.

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

[20]  M. Regenmortel Molecular design versus empirical discovery in peptide-based vaccines. Coming to terms with fuzzy recognition sites and ill-defined structure-function relationships in immunology. , 1999 .

[21]  M. Bhasin,et al.  Bcipep: A database of B-cell epitopes , 2005, BMC Genomics.

[22]  Darren R Flower,et al.  Immunoinformatics and the prediction of immunogenicity. , 2002, Applied bioinformatics.

[23]  A. Osterhaus,et al.  First peptide vaccine providing protection against viral infection in the target animal: studies of canine parvovirus in dogs , 1994, Journal of virology.

[24]  Christopher J. Oldfield,et al.  Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling , 2005, Journal of molecular recognition : JMR.

[25]  Channa K. Hattotuwagama,et al.  AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data , 2005, Immunome research.

[26]  M. Lehtinen,et al.  Synthetic peptides as diagnostic tools in virology. , 1993, Advances in virus research.

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

[28]  E Westhof,et al.  PREDITOP: a program for antigenicity prediction. , 1993, Journal of molecular graphics.

[29]  M.H.V. Van Regenmortel,et al.  Antigenicity and immunogenicity of synthetic peptides. , 2001 .

[30]  M. V. Regenmortel,et al.  Chapter 4 - Peptide immunoassays , 1999 .

[31]  M. H. Regenmortel Chapter 8 – Synthetic peptides as vaccines , 1999 .

[32]  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.

[33]  F. Brown,et al.  Protection of swine from foot-and-mouth disease with one dose of an all-D retro peptide. , 1999, Vaccine.

[34]  Richard A. Lerner,et al.  Immunogenic structure of the influenza virus hemagglutinin , 1982, Cell.

[35]  S. Kennel,et al.  Binding of monoclonal antibody to protein antigen in fluid phase or bound to solid supports. , 1982, Journal of immunological methods.

[36]  D. Laune,et al.  Systematic Exploration of the Antigen Binding Activity of Synthetic Peptides Isolated from the Variable Regions of Immunoglobulins* , 1997, The Journal of Biological Chemistry.

[37]  G. Air,et al.  Epitopes on protein antigens: Misconceptions and realities , 1990, Cell.

[38]  R. Lerner,et al.  The chemistry and mechanism of antibody binding to protein antigens. , 1988, Advances in immunology.

[39]  T. Pinheiro,et al.  Analysis of a 17-amino acid residue, virus-neutralizing microantibody. , 2005, The Journal of general virology.

[40]  M. V. Regenmortel,et al.  Antigenic cross-reactivity potential of synthetic peptides immobilized on polyethylene rods. , 1991, Molecular immunology.

[41]  M. Luscher,et al.  Conformational constraints imposed on a pan-neutralizing HIV-1 antibody epitope result in increased antigenicity but not neutralizing response. , 2005, Vaccine.

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

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

[44]  J. Berzofsky,et al.  Adsorption of the protein antigen myoglobin affects the binding of conformation-specific monoclonal antibodies. , 1988, Biophysical journal.

[45]  M. V. Regenmortel,et al.  Reductionism and complexity in molecular biology , 2004, HIV/AIDS: Immunochemistry, Reductionism and Vaccine Design.

[46]  Avner Schlessinger,et al.  Epitome: database of structure-inferred antigenic epitopes , 2005, Nucleic Acids Res..

[47]  Erwin L Roggen,et al.  An in silico method using an epitope motif database for predicting the location of antigenic determinants on proteins in a structural context , 2006, Journal of molecular recognition : JMR.

[48]  J. Berzofsky Intrinsic and extrinsic factors in protein antigenic structure. , 1985, Science.

[49]  B. Wahrén,et al.  A complementarity-determining region synthetic peptide acts as a miniantibody and neutralizes human immunodeficiency virus type 1 in vitro. , 1993, Proceedings of the National Academy of Sciences of the United States of America.