Contents Preface.xvii Acknowledgements .xix Author .xxi About the Book . xxiii List of Abbreviations.xxv Chapter 1 Overview of Immunology and Computational Immunology .1 1.1 Introduction .

1 1.2 History of the Science of Immunology .1 1.3 Innate Immune System .8 1.3.1 Physical Barriers .9 1.

3.2 Cellular Components . 10 1.3.3 Cytokines . 11 1.3.4 The Complement System .

12 1.3.5 Cellular Receptors . 12 1.3.5.1 Toll-Like Receptor . 12 1.

3.5.2 NOD-Like Receptors . 13 1.3.5.3 Plasma Proteins. 13 1.

4 Adaptive Immune System . 13 1.5 Clonal Selection . 15 1.6 Antigen . 16 1.7 Immune Cells and Organs . 16 1.

8 Antigen Processing and Presentation . 18 1.9 Antibody-Dependent Cellular Cytotoxicity . 19 1.10 Immunodeficiencies . 19 1.11 Immune Tolerance and Autoimmunity . 19 1.

12 Hypersensitivity/Allergy .20 1.13 Infection .20 1.14 Vaccination .20 1.15 Tracing the Origin of the Applications of the Science of Computation in Science, Biology, and Immunology . 21 1.

16 History of Computational Immunology . 21 1.17 The Current Developments of Computational Immunology .22 1.18 Different Immunological Databases .23 1.19 Computational Immunology and the Biology of Disease .24 1.

20 Discussions .25 References .26 Chapter 2 Immune Organs and Cells, Antigen, and Antibody, B-Cell, and T-Cell Development .29 2.1 Introduction .29 2.2 Immune Cells and Organs .29 2.

2.1 Stem Cells .29 2.2.1.1 Computational Immunology and Haematopoiesis . 31 2.2.

2 Cells of the Immune System . 31 2.2.2.1 Lymphocytes . 32 2.2.2.

2 Lymphocytes Types and Function . 32 2.2.2.3 Monocytes.38 2.2.2.

4 Macrophages .38 2.2.2.5 Granulocytes . 39 2.2.2.

6 Mast Cells .40 2.2.2.7 Dendritic Cells . 41 2.2.2.

8 Primary Lymphoid Organs . 42 2.2.2.9 Secondary Lymphoid Organs . 45 2.3 Antigen . 47 2.

3.1 Epitopes .48 2.3.2 Paratope .49 2.3.3 Immunogenicity .

49 2.3.4 Antigenicity .50 2.3.5 Types of Antigen .50 2.3.

6 Antigen Receptors . 51 2.3.6.1 B-Cell Receptors . 51 2.3.6.

2 T-Cell Receptors . 51 2.3.6.3 Preformed Receptors . 52 2.3.6.

4 Comparison of BCR and TCR . 52 2.4 Immunoglobulin . 52 2.4.1 Immunoglobulin Structure . 53 2.4.

2 Immunoglobulin Function .54 2.4.2.1 Antigen Binding .54 2.4.2.

2 Effector Functions . 55 2.4.3 Immunoglobulin Classes . 55 2.4.4 Immunoglobulin Types and Subtypes .56 2.

4.5 Isotypes .56 2.4.5.1 IgG .56 2.4.

5.2 IgM . 57 2.4.5.3 IgA . 57 2.4.

5.4 IgD . 57 2.4.5.5 IgE . 57 2.4.

6 Antigenic Determinants . 58 2.4.6.1 Isotype . 58 2.4.6.

2 Idiotype . 58 2.4.6.3 Allotype . 59 2.4.7 Antigen-Antibody Reactions: Lock and Key Concept .

59 2.4.8 Non-covalent Bonds . 59 2.4.9 Affinity . 59 2.4.

10 Avidity . 59 2.4.11 Specificity .60 2.4.12 Cross Reactivity .60 2.

5 B-Cell Development .60 2.5.1 Antigen-Independent Phase .