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فهرست مطالب: Preface . . . . . . . . . . . . . . vContributors . . . . . . . . . . . . . . . xi PART I INFORMATION OF ANTIBODY SEQUENCES AND STRUCTURES 1 Antibody Sequence and Structure Analyses Using IMGT®: 30 Years of Immunoinformatics . . . . . . . . 3 Marie-Paule Lefranc and Ge´rard Lefranc 2 Structural Classification of CDR-H3 in Single-Domain VHH Antibodies . 61 Daisuke Kuroda and Kouhei Tsumoto PART II MODELING ANTIBODY STRUCTURES AND DYNAMICS 3 Computational Modeling of Antibody and T-Cell Receptor (CDR3 Loops) . . . . . . . . . 83 Frederikke I. Marin and Paolo Marcatili 4 Molecular Dynamics Simulation for Investigating Antigen–Antibody Interaction . . . . . . . . . 101 Takefumi Yamashita 5 Molecular Dynamics Methods for Antibody Design . . . . . 109 Matthew Carter Childers and Valerie Daggett 6 Probing Conformational Dynamics of Antibodies with Geometric Simulations . . . . . . . . . . . 125 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 . . . . . . . . . 143 Shide Liang and Chi Zhang 8 Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations . . . . . . 151 Gert-Jan Bekker and Narutoshi Kamiya 9 Assessing and Engineering Antibody Stability Using Experimental and Computational Methods . . . . . . . . . . 165 Cheng Zhang and Paul Anthony Dalby 10 In Silico Prediction Method for Protein Asparagine Deamidation . . . 199 Lei Jia and Yaxiong Sun viiviii Contents 11 Structure-Based Optimization of Antibody-Based Biotherapeutics for Improved Developability: A Practical Guide for Molecular Modelers . . . . . . . . . . 219 Nels Thorsteinson, Stephen R. Comeau Jr, and Sandeep Kumar PART IV PREDICTION OF ANTIBODY-ANTIGEN INTERACTIONS 12 B-Cell Epitope Predictions Using Computational Methods . . . 239 Dandan Zheng, Shide Liang, and Chi Zhang 13 Computational Epitope Prediction and Design for Antibody Development and Detection . . . . . . . . . . 255 Riccardo Capelli, Stefano A. Serapian, and Giorgio Colombo 14 Information-Driven Antibody–Antigen Modelling with HADDOCK . . . . 267 Francesco Ambrosetti, Zuzana Jandova, and Alexandre M. J. J. Bonvin 15 Structural Modeling of Adaptive Immune Responses to Infection . . . 283 Tina Lusiany, Zichang Xu, Dianita S. Saputri, Hendra S. Ismanto, Sedat Aybars Nazlica, and Daron M. Standley 16 Protein–Protein Interaction Modelling with the Fragment Molecular Orbital Method . . . . . . . . . . . . 295 Shigenori Tanaka PART V COMPUTER-AIDED ANTIBODY AFFINITY MATURATION AND BEYOND 17 Structural Considerations in Affinity Maturation of Antibody-Based Biotherapeutic Candidates . . . . . . . . . . . . 309 Stephen R. Comeau, Nels Thorsteinson, and Sandeep Kumar 18 Structure-Based Affinity Maturation of Antibody Based on Double-Point Mutations . . . . . . . . . . . 323 Shuntaro Chiba, Yasushi Okuno, and Masateru Ohta 19 Antibody Affinity Maturation Using Computational Methods: From an Initial Hit to Small-Scale Expression of Optimized Binders . . . . . . 333 Barbara Medagli, Miguel A. Soler, Rita De Zorzi, and Sara Fortuna 20 Optimizing Antibody–Antigen Binding Affinities with the ADAPT Platform . . . . . . . . . . . . 361 Traian Sulea, Christophe Deprez, Christopher R. Corbeil, and Enrico O. Purisima 21 Using Graph-Based Signatures to Guide Rational Antibody Engineering . 375 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 . . . . . . . 399 Simone Conti and Martin KarplusContents ix 23 Analytical Method for Experimental Validation of Computer-Designed Antibody . . . . . . . . . . . 409 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 . . . . . . . 437 Hung-Pin Peng and An-Suei Yang 25 Bioinformatic Analysis of Natively Paired VH:VL Antibody Repertoires for Antibody Discovery . . . . . . . . . . 447 Ahmed S. Fahad, Bharat Madan, and Brandon J. DeKosky 26 Analyzing Antibody Repertoire Using Next-Generation Sequencing and Machine Learning . . . . . . . . . . . 465 Shuto Hayashi and Shumpei Ishikawa 27 A Computational Pipeline for Predicting Cancer Neoepitopes . . . . . . 475 Anna-Lisa Schaap-Johansen and Paolo Marcatili Index . . . . . . . . . . . . . . . 489 مشخصات فایل |
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| عنوان (Title): | Computer-Aided Antibody Design |
| نام فایل (File name): | 955-www.GeneProtocols.ir-Computer-Aided Antibody Design-Humana Press (2022).pdf |
| عنوان فارسی (Title in Persian): |
طراحی آنتی بادی به کمک کامپیوتر
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| ایجاد کننده: | Kouhei Tsumoto, Daisuke Kuroda |
| زبان (Language): | انگلیسی English |
| سال انتشار: | 2022 |
| شابک ISBN: | 1071626086, 9781071626085 |
| نوع سند (Doc. type): | کتاب |
| فرمت (File extention): | |
| حجم فایل (File size): | 21.6 مگابایت |
| تعداد صفحات (Book length in pages): | 481 |
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برچسب ها:
2022,
آنتی بادی,
انگلیسی,
ایمونولوژی,
بیوانفورماتیک,
سیستم ایمنی,
پروتکل بیوشیمی,
پروتکل پزشکی,
