Immunoinformatics (eBook)

Christian Schönbach is currently an Associate Professor (Genetics and Genomics) at Nanyang Technological University (Singapore). Until recently he was Team Leader of the Immunoinformatics Team at the RIKEN Genomic Sciences Center (Japan). His research on decoding mouse genome information employs both computational and experimental methods. He obtained is higher education at University of Würzburg, SUNY Albany, University of Tübingen, Max-Planck Institute for Biology, and UCSD. He holds a doctor degree in Genetics obtained through immunogenetics research under Jan Klein at the Max-Planck Institute for Biology. He completed his post-doctoral training in experimental and computational immunology with Masafumi Takiguchi and Kohji Egawa at The University of Tokyo, Institute of Medical Science. His working experience includes research scientist in gene discovery and bioinformatics at Chugai Research Institute for Molecular Medicine, Inc. (Japan), visiting scientist in immunology at the University of Tokyo, principal investigator in computational immunology at Kent Ridge Digital Labs, and Team Leader at RIKEN GSC where he interfaced for its bioinformatics group between computer science and experimental biology. Besides he contributed to the RIKEN GSC large-scale project ‘Functional Annotation of Mouse’ as a senior annotation manager and core group member. C. Schönbach authored 55 publications and two patents. He is a founding member of the International Immunomics Society, section editor for Immunome Research and served as editorial board member of New Generation Computing. He contributed as program committee member to various international bioinformatics meetings and to international conferences as invited speaker, keynote speaker, and memorial lecturer. In 2004 he convened the 1st International Immunoinformatics Symposium at RIKEN GSC. Shoba Ranganathan is currently Chair Professor of Bioinformatics at Macquarie University (Australia). She is also Adjunct Professor at the National University of Singapore. Her research is focused on bioinformatics analysis at the genome, transcriptome and proteome levels. She holds a doctorate degree in Chemistry from the Indian Institute of Technology, Delhi, India under the supervision of A.S.N. Murthy, followed by post-doctoral training in biocomputing with Bernard Pullamn and Alberte Pullman at the Institut de Biologie Physico-Chimique, Paris, France. Her working experience includes academic positions at the University of New Orleans, USA; University of Delhi, India; University of Sydney, Australia; Australian National University and the National University of Singapore, Singapore. S. Ranganathan has authored 77 publications. She was the first Australian Director elected to the Board of the International Society for Computational Biology (ISCB) and is currently the President, Asia-Pacific Bioinformatics Network (APBionet) and Steering Committee member of the International Immunomics Society. She is an editorial board member and reviewer for several bioinformatics journals and has served on the organizing committee of various international conferences. Vladimir Brusic is the Director of Bioinformatics, Cancer Vaccine Centre, Dana Farber Cancer Institute, Boston, Massachusetts USA, the Professor of Bioinformatics and Database Management at the University of Queensland, Brisbane Australia, and an Adjunct Associate Professor at The National University of Singapore. His research is focused on translational bioinformatics, particularly applications in immunomics and vaccine development. He has been a pioneer in the field of immunoinformatics and introduced the use of several machine learning techniques into the study of immunology. He has a PhD from LaTrobe University, Australia. He has master degrees in Biomedical Engineering, Applied Science, and Business Administration. He worked at University of Belgrade (Serbia), Walter and Eliza Hall Institute (Australia), and Institute for Infocomm Research (Singapore). Dr Brusic published more than 130 scientific articles and two patents. He is the founding Vice-president of the international Immunomics Society. He is a member of editorial boards and reviewer for several journals and has served on the program committees of numerous international conferences.

Foreword 5
Contents 8
Contributors 15
IMGT-ONTOLOGY, IMGT® Databases, Tools, and Web Resources for Immunoinformatics 18
1.1 Introduction 18
1.2 The IMGT® Information System 19
1.3 IMGT-ONTOLOGY Concepts and IMGT® Components for Genomics 22
1.4 IMGT-ONTOLOGY Concepts and IMGT® Components for Genetics 23
1.5 IMGT-ONTOLOGY Concepts and IMGT® Components for 2D and 3D Structures 27
1.6 IMGT-Choreography 29
1.7 Conclusions 30
1.8 Citing IMGT 31
Acknowledgements 31
References 32
IMGT Standardization for Molecular Characterization of the T Cell Receptor/ Peptide/ MHC Complexes 36
2.1 Introduction 36
2.2 T Cell Receptor/Peptide/MHC 3D Structures and IMGT Standardization 38
2.3 TR/pMHC Contact Analysis 45
2.4 Conclusions 62
2.5 Citing IMGT/3Dstructure-DB 62
Acknowledgements 62
References 63
Structural Immunoinformatics 67
3.1 Introduction 67
3.2 Structural Features of MHC Peptides 68
3.3 MHC-Peptide Interaction Parameters 69
3.4 Structural Prediction Techniques 70
3.5 Application of Docking Protocol 74
3.6 Available Resources 75
3.7 Conclusions 76
References 76
In Silico QSAR-Based Predictions of Class I and Class II MHC Epitopes 78
4.1 Introduction 79
4.2 Methodology 81
4.3 Results 85
4.4 Discussion 93
4.5 Conclusions 100
References 101
Allergen Bioinformatics 105
5.1 Introduction 105
5.2 Allergen Databases 107
5.3 Allergenicity Prediction 114
5.4 Conclusion 118
Acknowledgements 118
References 119
Immunoinformatics Applied to Modifying and Improving Biological Therapeutics 122
6.1 Introduction 122
6.2 Components of the Immune Response to Biologicals 124
6.3 A New Concept: Deimmunization by T-Cell Epitope Modification 130
6.4 A Step-by-Step Approach to Deimmunization 135
6.5. When Can Deimmunization Be Useful? 140
6.6 Conclusions 141
References 141
Plasticity of Dendritic Cell Transcriptional Responses to Antigen: Functional States of Dendritic Cells 145
7.1 Introduction 145
7.2 Dendritic Cells 146
7.3 Gene Expression Programs in Antigen-Presenting Cells 150
7.4 Integrating Genomics Data: A System View of the Immune Response 153
7.5 Conclusions 156
Acknowledgements 156
References 157
Understanding the Immune System by Computer- Aided Modeling 159
8.1 Introduction 159
8.2 Computational Immunology 160
8.3 Discrete Models of HIV Infection 165
8.4 Simulation of HIV-1 Infection 166
8.5 Conclusions 169
References 169
Simulation of HIV-1 Molecular Evolution in Response to Chemokine Coreceptors and Antibodies 172
9.1 Introduction 172
9.2 The HIV Replication Cycle 173
9.3 The Model 175
9.4 Simulations 179
9.5 Conclusions and Future Directions 187
Acknowledgements 188
References 188
MUTANT MOUSE: Biosimulator for the Functional Annotation of Gene and Genome Networks 190
10.1 Introduction 190
10.2 I/O System in Mouse Genetics 192
10.3 Renaissance of Classical Genetics 195
10.4 Conclusions 203
Acknowledgements 204
References 204
Index 206