Main description:

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.

Contents:

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