Computer-aided antibody design

著者

• 津本, 浩平 ツモト, コウヘイ
• 黒田, 大祐 クロダ, ダイスケ

書誌事項

Computer-aided antibody design

edited by Kouhei Tsumoto, Daisuke Kuroda

（Methods in molecular biology / John M. Walker, series editor, 2552）（Springer protocols）

Humana Press, c2023

注記

Includes bibliographical references and index

内容説明・目次

内容説明

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 International License via link.springer.com.

目次

PART I INFORMATION OF ANTIBODY SEQUENCES AND STRUCTURES 1. Antibody sequence and structure analyses using IMGT (R): 30 years of immunoinformatics Marie-Paule Lefranc and Gerard Lefranc 2. Structural Classification of CDR-H3 in Single-Domain VHH Antibodies Daisuke Kuroda and Kouhei Tsumoto PART II MODELING ANTIBODY STRUCTURES AND DYNAMICS 3. Computational modelling of Antibody and T Cell receptor (CDR3 loops) Frederikke I. Marin and Paolo Marcatili 4. Molecular dynamics simulation for investigating antigen-antibody interaction Takefumi Yamashita 5. Molecular Dynamics Methods for Antibody Design Matthew Carter Childers and Valerie Daggett 6. Probing antibody dynamics with geometric simulations Andrejs Tucs, Koji Tsuda and Adnan Sljoka PART III PREDICTION AND OPTIMIZATION OF BIOLOGICAL AND BIOPHYSICAL PROPERTIES OF ANTIBODIES 7. PITHA: a webtool to predict immunogenicity for humanized and fully human therapeutic antibodies Shide Liang and Chi Zhang 8. Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations Gert-Jan Bekker and Narutoshi Kamiya 9. Assessing and engineering antibody stability using experimental and computational methods Cheng Zhang and Paul Dalby 10. In Silico Prediction Method for Protein Asparagine Deamidation Lei Jia and Yaxiong Sun 11. Structure-based Optimization of Antibody-Based Biotherapeutics for Improved Developability: A Practical Guide for Molecular Modelers Nels Thorsteinson, Stephen R. Comeau, Jr., Sandeep Kumar PART IV PREDICTION OF ANTIBODY-ANTIGEN INTERACTIONS 12. B-cell epitope predictions using computational methods Dandan Zheng, Shide Liang, Chi Zhang 13. Computational Epitope Prediction and Design for Antibody Development and Detection Riccardo Capelli, Stefano A. Serapian, and Giorgio Colombo 14. Information-driven antibody-antigen modelling with HADDOCK Francesco Ambrosetti , Zuzana Jandova, and Alexandre M.J.J. Bonvin 15. Structural modeling of adaptive immune responses to infection Tina Lusiany, Zichang Xu, Dianita S. Saputri, Hendra S. Ismanto, Sedat Aybars Nazlica, Daron M. Standley 16. Protein-Protein Interaction Modelling with the Fragment Molecular Orbital Method Shigenori Tanaka PART V COMPUTER-AIDED ANTIBODY AFFINITY MATURATION AND BEYOND 17. Structural Considerations in Affinity Maturation of Antibody-Based Biotherapeutic Candidates Stephen R. Comeau, Jr., Nels Thorsteinson, and Sandeep Kumar 18. Structure-based affinity maturation of antibody based on double-point mutations Shuntaro Chiba, Yasushi Okuno, and Masateru Ohta 19. Antibody affinity maturation using computational methods: from an initial hit to small scale expression of optimised binders Barbara Medagli, Miguel A. Soler, Rita de Zorzi, and Sara Fortuna 20. Optimizing Antibody-Antigen Binding Affinities with the ADAPT Platform Traian Sulea, Christophe Deprez, Christopher R. Corbeil and Enrico O. Purisima 21. Using graph-based signatures to guide rational antibody engineering David B. Ascher, Lisa M. Kaminskas, YooChan Myung, and Douglas E.V. Pires 22. A computational framework for determining the breadth of antibodies against highly mutable pathogens Simone Conti and Martin Karplus 23. Analytical method for experimental validation of computer-designed antibody Aki Tanabe and Kouhei Tsumoto PART VI SYNTHETIC ANTIBODY LIBRARY, NEXT GENERATION SEQUENCING OF B-ELL REPERTOIRES AND IMMUNOTHERAPY 24. Computational analysis of antibody paratopes for antibody sequences in antibody libraries Hung-Pin Peng and An-Suei Yang 25. Bioinformatic Analysis of Natively Paired VH:VL Antibody Repertoires for Antibody Discovery Ahmed S. Fahad, Bharat Madan, and Brandon J. DeKosky 26. Analyzing antibody repertoire using next-generation sequencing and machine learning Shuto Hayashi and Shumpei Ishikawa 27. A computational pipeline for predicting cancer neoepitopes Anna-Lisa Schaap-Johansen and Paolo Marcatili

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詳細情報

• NII書誌ID(NCID): BD00894108
• ISBN:
  • 9781071626085
• 出版国コード: us
• タイトル言語コード: eng
• 本文言語コード: eng
• 出版地: New York
• ページ数/冊数: xiv, 491 p.
• 大きさ: 27 cm
• 分類:
  • DC23 : 616.0798
• 件名:
  • LCSH : Immunoglobulins -- Computer-aided design
• 親書誌ID:
  • BA10794673
  • BA88873632