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Computer-Aided Antibody Design

  • Book
  • © 2023

Overview

Editors:
  1. Kouhei Tsumoto

    1. School of Engineering, The University of Tokyo, Tokyo, Japan

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    You can also search for this editor in PubMed   Google Scholar

  2. Daisuke Kuroda

    1. School of Engineering, The University of Tokyo, Tokyo, Japan

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2552)

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Table of contents (27 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Information of Antibody Sequences and Structures

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Antibody Sequence and Structure Analyses Using IMGT®: 30 Years of Immunoinformatics

      • Marie-Paule Lefranc, Gérard Lefranc
      Pages 3-59

    3. Structural Classification of CDR-H3 in Single-Domain VHH Antibodies

      • Daisuke Kuroda, Kouhei Tsumoto
      Pages 61-79Open Access

  3. Modeling Antibody Structures and Dynamics

    1. Front Matter

      Pages 81-81
      Download chapter PDF

    2. Computational Modeling of Antibody and T-Cell Receptor (CDR3 Loops)

      • Frederikke I. Marin, Paolo Marcatili
      Pages 83-100

    3. Molecular Dynamics Simulation for Investigating Antigen–Antibody Interaction

      • Takefumi Yamashita
      Pages 101-107

    4. Molecular Dynamics Methods for Antibody Design

      • Matthew Carter Childers, Valerie Daggett
      Pages 109-124

    5. Probing Conformational Dynamics of Antibodies with Geometric Simulations

      • Andrejs Tucs, Koji Tsuda, Adnan Sljoka
      Pages 125-139

  4. Prediction and Optimization of Biological and Biophysical Properties of Antibodies

    1. Front Matter

      Pages 141-141
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    2. PITHA: A Webtool to Predict Immunogenicity for Humanized and Fully Human Therapeutic Antibodies

      • Shide Liang, Chi Zhang
      Pages 143-150

    3. Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations

      • Gert-Jan Bekker, Narutoshi Kamiya
      Pages 151-163

    4. Assessing and Engineering Antibody Stability Using Experimental and Computational Methods

      • Cheng Zhang, Paul Anthony Dalby
      Pages 165-197

    5. In Silico Prediction Method for Protein Asparagine Deamidation

      • Lei Jia, Yaxiong Sun
      Pages 199-217

    6. Structure-Based Optimization of Antibody-Based Biotherapeutics for Improved Developability: A Practical Guide for Molecular Modelers

      • Nels Thorsteinson, Stephen R. Comeau Jr, Sandeep Kumar
      Pages 219-235

  5. Prediction of Antibody-Antigen Interactions

    1. Front Matter

      Pages 237-237
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    2. B-Cell Epitope Predictions Using Computational Methods

      • Dandan Zheng, Shide Liang, Chi Zhang
      Pages 239-254

    3. Computational Epitope Prediction and Design for Antibody Development and Detection

      • Riccardo Capelli, Stefano A. Serapian, Giorgio Colombo
      Pages 255-266

    4. Information-Driven Antibody–Antigen Modelling with HADDOCK

      • Francesco Ambrosetti, Zuzana Jandova, Alexandre M. J. J. Bonvin
      Pages 267-282

    5. Structural Modeling of Adaptive Immune Responses to Infection

      • Tina Lusiany, Zichang Xu, Dianita S. Saputri, Hendra S. Ismanto, Sedat Aybars Nazlica, Daron M. Standley
      Pages 283-294
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Keywords

About this book

This volume details state-of-the- art methods on computer-aided antibody design. Chapters guide readers through information on antibody sequences and structures,  modeling antibody structures and dynamics, prediction and optimization of biological and biophysical properties of antibodies, prediction of antibody-antigen interactions, and computer-aided antibody affinity maturation and beyond. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

Authoritative and cutting-edge, Computer-Aided Antibody Design aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge. 

Chapter 2 is available open access under a Creative Commons Attribution 4.0 InternationalLicense via link.springer.com.

Editors and Affiliations

  • School of Engineering, The University of Tokyo, Tokyo, Japan

    Kouhei Tsumoto, Daisuke Kuroda

Bibliographic Information

  • Book Title: Computer-Aided Antibody Design

  • Editors: Kouhei Tsumoto, Daisuke Kuroda

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2609-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-2608-5Published: 09 November 2022

  • Softcover ISBN: 978-1-0716-2611-5Published: 10 November 2023

  • eBook ISBN: 978-1-0716-2609-2Published: 08 November 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 491

  • Number of Illustrations: 21 b/w illustrations, 118 illustrations in colour

  • Topics: Antibodies, Bioinformatics, Pharmaceutical Sciences/Technology

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