Computer-Aided Vaccine Design

Dr Joo Chuan Tong is a Senior Scientist at the A*STAR Institute of High Performance Computing, Singapore. He is an Adjunct Assistant Professor at the Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore. Dr. Tong has won numerous awards, including the MIT TR35 Award in 2008 and Singapore Youth Award (Science and Technology) in 2009, and is the only Asian on the Senior Innovation Advisory Board of Pfizer Inc, the world's largest research-based pharmaceutical company, at their world headquarters in New York, USA.

Computational pre-screening of antigens is now routinely applied to the discovery of vaccine candidates.Computer-aided vaccine design is a comprehensive introduction to this exciting field of study. The book is intended to be a textbook for researchers and for courses in bioinformatics, as well as a laboratory reference guide. It is written mainly for biologists who want to understand the current methods of computer-aided vaccine design. The contents are designed to help biologists appreciate the underlying concepts and algorithms used, as well as limitations of the methods and strategies for their use. Chapters include: MHC and T cell responses; Immunoglobulins and B cell responses; Scientific publications and databases; Database design; Computational T cell vaccine design; Computational B cell vaccine design; infectious disease informatics; Vaccine safety and quality assessments; and Vaccine adjuvant informatics.

List of figures

List of abbreviations

About the authors

Preface

Chapter 1: MHC and T cell responses

Abstract:

1.1 Genetic organization of the MHC

1.2 MHC structure

1.3 MHC function

1.4 Peptide binding

Chapter 2: Immunoglobulins and B cell responses

Abstract:

2.1 Types of immunoglobulins

2.2 Immunoglobulin structure

2.3 Immunoglobulin function

2.4 Antigen binding

Chapter 3: Scientific publications and databases

Abstract:

3.1 Bibliographical information

3.2 Searching the literature

3.3 General databases containing information on genes and proteins

3.4 Immunological databases

3.5 Small molecule databases

Chapter 4: Database design

Abstract:

4.1 Fundamentals of database design

4.2 ER diagram

4.3 Normalization and normal forms

Chapter 5: Computational T cell vaccine design

Abstract:

5.1 Sequence-based methods

5.2 Structure-based methods

5.3 Broad-based T cell vaccine design

Chapter 6: Computational B cell vaccine design

Abstract:

6.1 Sequence-based methods

6.2 Structure-based methods

Chapter 7: Infectious disease informatics

Abstract:

7.1 Infectious diseases in history

7.2 Microbial sequence analysis

7.3 Detecting natural selection in molecular evolution

Chapter 8: Vaccine safety and quality assessments

Abstract:

8.1 Assessment of ADME/Tox deficiencies

8.2 Assessment of allergenicity

Chapter 9: Vaccine adjuvant informatics

Abstract:

9.1 Virtual combinatorial library

9.2 Chemical file formats

9.3 Considerations for virtual library design

Index