Antigen–Antibody Interaction Database (AgAbDb): A Compendium of Antigen–Antibody Interactions

  • Urmila Kulkarni-Kale
  • Snehal Raskar-Renuse
  • Girija Natekar-Kalantre
  • Smita A. Saxena
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1184)

Abstract

Antigen–Antibody Interaction Database (AgAbDb) is an immunoinformatics resource developed at the Bioinformatics Centre, University of Pune, and is available online at http://bioinfo.net.in/AgAbDb.htm. Antigen–antibody interactions are a special class of protein–protein interactions that are characterized by high affinity and strict specificity of antibodies towards their antigens. Several co-crystal structures of antigen–antibody complexes have been solved and are available in the Protein Data Bank (PDB). AgAbDb is a derived knowledgebase developed with an objective to compile, curate, and analyze determinants of interactions between the respective antigen–antibody molecules. AgAbDb lists not only the residues of binding sites of antigens and antibodies, but also interacting residue pairs. It also helps in the identification of interacting residues and buried residues that constitute antibody-binding sites of protein and peptide antigens. The Antigen–Antibody Interaction Finder (AAIF), a program developed in-house, is used to compile the molecular interactions, viz. van der Waals interactions, salt bridges, and hydrogen bonds. A module for curating water-mediated interactions has also been developed. In addition, various residue-level features, viz. accessible surface area, data on epitope segment, and secondary structural state of binding site residues, are also compiled. Apart from the PDB numbering, Wu–Kabat numbering and explicit definitions of complementarity-determining regions are provided for residues of antibodies. The molecular interactions can be visualized using the program Jmol. AgAbDb can be used as a benchmark dataset to validate algorithms for prediction of B-cell epitopes. It can as well be used to improve accuracy of existing algorithms and to design new algorithms. AgAbDb can also be used to design mimotopes representing antigens as well as aid in designing processes leading to humanization of antibodies.

Key words

Antigen Antibody Antigen–antibody complex Antigen–antibody interactions B-cell epitope Paratope Antibody-binding site Conformational or discontinuous epitope Immunoinformatics Bioinformatics Derived database 

Abbreviations

AAIF

Antigen–Antibody Interaction Finder

Ab

Antibody

Ag

Antigen

Ag–Ab

Antigen–antibody

AgAbDb

Antigen–Antibody Interaction Database

ASA

Accessible surface area

BR

Buried residue

BS

Binding site

CDR

Complementarity-determining region on heavy chain

CE

Conformational epitope

CEP

Conformational epitope prediction

Ig

Immunoglobulin

IR

Interacting residues

LDR

Complementarity-determining region on light chain

PDB

Protein Data Bank

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Urmila Kulkarni-Kale
    • 1
  • Snehal Raskar-Renuse
    • 1
    • 2
  • Girija Natekar-Kalantre
    • 1
    • 3
  • Smita A. Saxena
    • 1
  1. 1.Bioinformatics CentreUniversity of PunePuneIndia
  2. 2.Agilent TechnologiesBangaloreIndia
  3. 3.Department of Chemical EngineeringIndian Institute of TechnologyMumbaiIndia

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