Computer-Aided Vaccine Design

Summary

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. Computer-Aided Vaccine Design 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. The book is of interest to computational biologists who would like to understand more about the biological concepts related to the field of computational immunology.

Key Features

• Essential for any biologists who wants to understand methods of computer-aided vaccine design and how the different computer programs work
• Available data sources and publicly available software are amply described, with detailed analysis of their strengths and weaknesses
• Theoretical concepts and practical examples of database design and development for a virtual screening campaign are provided
• Underlying algorithms and assumptions are clearly explained for the non-specialist
• Theoretical foundations are linked to the design of a virtual screening campaign, with an emphasis on potential problems and solutions

Content

• Computer-aided vaccine design: its nature and scope - history of vaccination and computer-aided vaccine design; introduction of adaptive immune system: antigen-processing pathway, immunoproteasome, transporter associated with antigen processing (TAP), major histocompatibility complex (MHC), MHC superfamilies, T cell receptor, promiscuous T cell antigens, B cell receptor and B cell antigens; introduction to terms and terminologies in computer-aided vaccine design
• Immunological databases - exploring the architectures of existing immunological databases: Immune Epitope Database and Analysis Resource (IEDB), SYFPEITHI, AntiJen, MHCBN, MHC-peptide Interaction Database (MPID-T), B-cell Epitope Interaction Database (BEID), ImMunoGeneTics information system (IMGT), among others; concepts of database design: describing entities and tables; describing attributes and columns; understanding data types; relationships and cardinality; describing primary, composite and foreign keys; normalization and normal forms; denormalization; identifying and resolving anomalies; understanding entity relationship modeling and implementing an immunological database
• Infectious disease informatics - infectious diseases in history; concepts of sequence analysis, phylogenetic trees, information entropy and their applications to infectious disease vaccine discovery; concepts and applications of mathematical models to study infectious disease transmissions, selection pressures of pathogens and spatio-temporal modeling of infectious disease evolution
• T cell vaccine design - concepts and applications of sequence-based methods of binding motifs, matrices, decision trees and machine-learning algorithms (i.e. support vector machines, artificial neural networks and hidden Markov models) for the discovery of T cell antigens in pathogens; concepts and applications of MHC superfamilies, promiscuous epitopes and application of MHC clustering techniques to broad based vaccine design; concepts and applications of structure-based methods of peptide threading, molecular docking and homology modeling for the discovery of T cell antigens in pathogens
• B cell vaccine design - concepts and applications of propensity scales and sequence-based methods of machine-learning algorithms (i.e. Naive Bayes classifiers, artificial neural networks, support vector machines and hidden Markov models) for mapping linear B cell epitopes; concepts and applications of secondary structure and 3-D substructure search algorithms for the discovery of non-linear B cell epitopes
• Vaccine safety and quality assessments - introduction to absorption, distribution, metabolism, excretion, toxicology (ADME/T) and in silico assessments of peptides and proteins; introduction to methods and protocols for assessing potential allergenicity and cross reactivity (autoimmunity) in vaccine candidates
• Adjuvant informatics - introduction to mathematical models and computational methods for adjuvant design, development and analysis

Readership

Researchers and post-graduate students in biology, bioinformatics, medical informatics and immunology, postgraduate and pharmaceutical industry.

Author

Chuan, Tong Joo Dr and Ranganathan, Shoba Professor
Tong Joo Chuan is currently a Principal Investigator and Assistant Department Head of the Data Mining Department at A*STAR Institute for Infocomm Research, Singapore. He is also 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. Current areas of research in the Tong group include: computational immunology, computational epigenetics, combinatorial library design and computational modeling of biological systems.

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, followed by post-doctoral training in biocomputing with Bernard Pullman and Alberte Pullman at the Institut de Biologie Physico-Chimique, Paris, France and at the University of New Orleans, USA. Her professional experience includes academic positions at the University of Delhi, India; University of Sydney, Australia; Australian National University and the National University of Singapore as well as Consultant to the first Australian bioinformatics company, eBioinformatics. 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. Professor Ranganathan has authored more than 100 publications. She is an editorial board member and reviewer for several bioinformatics journals and has served on the organizing/program committees of several international conferences.