Structural Characterization of Peptide Antibodies

Part of the Methods in Molecular Biology book series (MIMB, volume 1348)


The role of proteins as very effective immunogens for the generation of antibodies is indisputable. Nevertheless, cases in which protein usage for antibody production is not feasible or convenient compelled the creation of a powerful alternative consisting of synthetic peptides. Synthetic peptides can be modified to obtain desired properties or conformation, tagged for purification, isotopically labeled for protein quantitation or conjugated to immunogens for antibody production. The antibodies that bind to these peptides represent an invaluable tool for biological research and discovery. To better understand the underlying mechanisms of antibody–antigen interaction here we present a pipeline developed by us to structurally classify immunoglobulin antigen binding sites and to infer key sequence residues and other variables that have a prominent role in each structural class.


Peptide antibody Structure Clustering Linear epitope 


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdenseDenmark
  2. 2.Center for Biological Sequence Analysis, Department of Systems BiologyTechnical University of DenmarkLyngbyDenmark

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