Main description:

This volume explores computational vaccine design and the technologies that support it. Chapters have been divided into four parts detailing immunonics and system immunology, databases, prediction of antigenicity and immunogenicity, and computational vaccinology. 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, Computational Vaccine Design: Methods and Protocols aims to reflect on the rigorous and imaginative use of computational technologies to help catalyze future efforts and to improve global public health through the development of a broad range of novel vaccines.

Contents:

1. Vaccine Design: an introduction

Pedro A Reche

PART I: IMMUNOMICS AND SYSTEM IMMUNOLOGY

2. Epitope binning of monoclonal and polyclonal antibodies by biolayer interferometry

Kaito Nagashima and Jarrod J. Mousa

3. Clustering and annotation of T-cell receptor repertoires

Sebastiaan Valkiers, Sofie Gielis, Vincent M.L. Van Deuren, Kris Laukens, and Pieter Meysman

4. Protocol for Classification Single Cell PBMC Types from Pathological Samples using Supervised Machine Learning

Minjie Lyu, Lin Xin, Huan Jin, Lou T. Chitkushev, Guanglan Zhang, Derin B. Keskin and Vladimir Brusic

5. Unbiased, high-throughput identification of T cell epitopes by ELISPOT

Paul V. Lehmann, Diana R. Roen, and Alexander A. Lehmann

6. CD4+ T cell epitope identification from complex parasite antigen mixtures

Miguel Alvaro-Benito, Friederike Ebner, Miriam Bertazzon, Eliot Morrison

7. Computational grafting of epitopes

Manish Manish, Smriti Mishra, Monika Pahuja, Ayush Anand, Naidu Subbarao and Ram Samudrala

8. Manufacture of Mesoporous Silicon Microparticles (MSMPs) as adjuvants for vaccine delivery

Ana Lopez-Gomez, Irene Real-Arevalo, Raul Martin-Palma, Eduardo Martinez-Naves, Manuel Gomez del Moral

PART II: DATABASES

9. IEDB and CEDAR: Two Sibling Databases to Serve the Global Scientific Community

Nina Blazeska, Zeynep Kosaloglu-Yalcin, Randi Vita1, Bjoern Peters and Alessandro Sette

10. Updates on databases of allergens and allergen-epitopes

Rajat Kanti Karkar, Nandini Ghosh, Gaurab Sircar, Sudipto Saha

11. TSNAD and TSNAdb: The useful toolkit and database for clinical application of tumor-specific neoantigens

Jingcheng Wu and Zhan Zhou

12. EPIPOX: A Resource facilitating epitope-vaccine design against human Pathogenic Orthopoxviruses

Laura Ballesteros-Sanabria, Hector F.Pelaez-Prestel, Pedro A. Reche1 and Esther M. Lafuente

PARTE III. PREDICTON OF ANTIGENICITY AND IMMUNOGENICITY: TOOLS AND PROTOCOLS

13. Prediction of linear B cell epitopes in proteins

Juan R. de los Toyos

14. Design of linear B-cell epitopes and evaluation of their antigenicity, allergenicity, and toxicity: an immunoinformatics approach

Vijaya Sai Ayyagar

15. NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II

Roc Farriol-Duran, Marina Vallejo-Valles, Pep Amengual-Rigo, Martin Floor and Victor Guallar

16. Prediction of TAP transport of peptides with variable length using TAPREG

Hector F. Pelaez-Prestel, Laura Ballesteros-Sanabria, Pedro A. Reche

17. Docking-based Prediction of Peptide Binding to MHC Proteins

Mariyana Atanasova and Irini Doytchinova

18. The PANDORA software for anchor-restrained peptide:MHC modelling

Dario F. Marzella, Giulia Crocioni, Farzaneh M. Parizi, Li C. Xue

19. Prediction of Peptide and TCR CDR3 Loops in Formation of Class I MHC-Peptide-TCR Complexes using Molecular Models with Solvation

Nairuti Milan Mehta, Yuhui Li, Vini Patel, Wanning Li, Noam Morningstar-Kywi, Mateusz Pospiech, Houda Alachkar, Ian S Haworth

20. Prediction of Bacterial Immunogenicity by Machine Learning Methods

Ivan Dimitrov and Irini Doytchinova

21. Vaxi-DL: an artificial Intelligence enabled platform for vaccine development

P Preeti, Swarsat Kaushik Nath, Nevidita Arambam, Trapti Sharma, Priyanka Ray Choudhury, Alakto Choudhury, Ulrich Strych, Peter J. Hotez, Maria Elena Bottazzi, Kamal Rawal

22. A web-based method for the identification of IL6 based immunotoxicity in vaccine candidates

Anjali Dhall, Sumeet Patiyal, Neelam Sharma, Salman Sadullah Usmani, and Gajendra Pal Singh Raghava

23. In silico tool for identification, designing and searching of IL13 inducing peptides in antigens

Shipra Jain, Anjali Dhall, Sumeet Patiyal, and Gajendra P. S. Raghava

PART IV: COMPUTATIONAL VACCINOLOGY APPLICATIONS AND PROTOCOLS

24. A lean Reverse Vaccinology pipeline with publicly available bioinformatic tools

Bart Bart Cuypers, Rino Rappuoli and Alessandro Brozzi

25. Immunoinformatics protocol to design multi-epitope subunit vaccines

Parismita Kalita, Aditya K. Padhi, and Timir Tripathi

26. In-silico Structure-based Vaccine Design

Sakshi Piplani, David Winkler, Yoshikazu Honda-Okubo, Varun Khanna, Nikolai Petrovsky

27. Reverse vaccinology for influenza A virus: from genome sequencing to vaccine design

Valentina Di Salvatore, Giulia Russo and Francesco Pappalardo

28. Immunoinformatics vaccine design for Zika virus

Ana Clara Antonelli, Vinnycius Pereira Almeida, Simone Fonseca

29. Immunoinformatics approaches in designing vaccines against COVID-19

Ankita Chakraborty, Jagadeesh Bayry, Suprabhat Mukherjee

30. A Sample Guideline for Reverse Vaccinology Approach for the Development of Subunit Vaccine using Varicella Zoster as a Model Disease

Elif Cireli and Levent Cavas

31. Computational Vaccine Design for Poxviridae Family Viruses

Abbas Khan, Dong-Qing Wei, and Muhammad Suleman

32. Computational prediction of Trypanosoma cruzi epitopes towards the generation of an epitope-based vaccine against Chagas disease

Albert Ros-Lucas, David Rioja-Soto, Joaquim Gascon, Julio Alonso-Padilla

33. Computational vaccine design for common allergens

Nandini Ghosh, Gaurab Sircar, Sudipto Saha