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Homology Modeling of Antibody Variable Regions: Methods and Applications

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Homology Modeling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2627))

Abstract

Adaptive immunity specifically protects us from antigenic challenges. Antibodies are key effector proteins of adaptive immunity, and they are remarkable in their ability to recognize a virtually limitless number of antigens. Fragment variable (FV), the antigen-binding region of antibodies, can be split into two main components, namely, framework and complementarity determining regions. The framework (FR) consists of light-chain framework (FRL) and heavy-chain framework (FRH). Similarly, the complementarity determining regions (CDRs) comprises of light-chain CDRs 1–3 (CDRs L1–3) and heavy-chain CDRs 1–3 (CDRs H1–3). While FRs are relatively constant in sequence and structure across diverse antibodies, sequence variation in CDRs leading to differential conformations of CDR loops accounts for the distinct antigenic specificities of diverse antibodies. The conserved structural features in FRs and conformity of CDRs to a limited set of standard conformations allow for the accurate prediction of FV models using homology modeling techniques. Antibody structure prediction from its amino acid sequence has numerous important applications including prediction of antibody-antigen interaction interfaces and redesign of therapeutically and biotechnologically useful antibodies with improved affinity. This chapter summarizes the current practices employed in the successful homology modeling of antibody variable regions and the potential applications of the generated homology models.

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Authors and Affiliations

  1. Department of Physics, Indian Institute of Science, Bengaluru, India

    Harsh Bansia & Suryanarayanarao Ramakumar

  2. Advanced Science Research Center at The Graduate Center of the City University of New York, New York, NY, USA

    Harsh Bansia

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  1. Harsh Bansia
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  2. Suryanarayanarao Ramakumar
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Correspondence to Harsh Bansia or Suryanarayanarao Ramakumar .

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Editors and Affiliations

  1. Faculty of Chemistry, University of Warsaw, Warsaw, Poland

    Sławomir Filipek

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Bansia, H., Ramakumar, S. (2023). Homology Modeling of Antibody Variable Regions: Methods and Applications. In: Filipek, S. (eds) Homology Modeling. Methods in Molecular Biology, vol 2627. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2974-1_16

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  • DOI: https://doi.org/10.1007/978-1-0716-2974-1_16

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2973-4

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