In June , the Theoretical Immunology Workshop was hosted in Santa Fe, New Mexico to discuss "the topics of immune surveillance, mathematical models of HIV infection, complexities of antigen-antibody systems, immune suppression and tolerance, and idiotypie networks. Created to "standardize and manage the complexity of the immunogenetics data" coming out of the lab, the information system went on to become an international public reference for genetic and proteomic data related to immunology. With modern software, an immunological question can be asked, the question can be interpreted into a computer-based computation or simulation, and the resulting data can then be output and analyzed for meaningful answers. T-cell receptors TCRs are molecular proteins vital to the immune response, and their diversity is estimated to ranges from to different clonotypes, highlighting the need for powerful computational tools to better understand their effects on immune response.
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Road, Kolkata , India. Email: ni. Abstract Genome sequencing of humans and other organisms has led to the accumulation of huge amounts of data, which include immunologically relevant data. A large volume of clinical data has been deposited in several immunological databases and as a result immunoinformatics has emerged as an important field which acts as an intersection between experimental immunology and computational approaches.
It not only helps in dealing with the huge amount of data but also plays a role in defining new hypotheses related to immune responses. This article reviews classical immunology, different databases and prediction tools. It also describes applications of immunoinformatics in designing in silico vaccination and immune system modelling. All these efforts save time and reduce cost.
The role of an immune system is to protect against diseases by identifying and killing pathogens. An immune system includes innate and adaptive components. According to the traditional dogma of immunology, vertebrates have both innate and adaptive immune systems whereas invertebrates possess only an innate immune system.
It provides the backbone on which the adaptive immune system was able to evolve. The innate immune system is less specific and works as a first line of defence. An adaptive immune response occurs against a pathogen within 5 or 6 days after the initial exposure to the pathogen. Functionally, it accounts for two inter-related activities: recognition and response. It can also recognize altered self cells, such as virus-infected self cells, and distinguish between healthy and cancerous cells.
However, it may not always recognize cancer cells as foreign or abnormal cells. As soon as the adaptive immune system recognizes a pathogen, an effector response is elicited to kill or neutralize it. The response is unique to defend against a particular type of pathogen. Later exposure to the same pathogen induces a heightened and more specific response because the adaptive immune system retains memory.
The adaptive immune system has two parts: the cellular immune response of T cells and the humoral response of B cells. B-cell epitopes can be linear and discontinuous amino acids. T-cell epitopes are short linear peptides. Most of the T cells can be in either of the two subsets, distinguished by the presence of one or other of two glycoproteins on their surface, designated as CD8 or CD4. A brief description of various components of the human immune system is provided as supplementary material.
The idea that the immune response exists in an organism is quite old. The earliest literary reference to immunology goes back to bc by Thucydides. The next major advancement in immunology came with the induction of immunity to cholera by Louis Pasteur. After applying weakened pathogen to animals, he administered in a dose of vaccine to a boy bitten by a rabid dog and the boy survived.
However, Pasteur could not explain its mechanism. In , experiments of Emil Von Behring and Shibasabura Kitasato led to the understanding of the mechanism of immunity. Their experiments described how antibodies present in the serum provided protection against pathogens. An immune system may be considered as a network of thousands of molecules, which leads to many intertwined responses.
It is structurally and functionally diverse and this diversity varies both between individuals and temporally within individuals. Huge amounts of data related to immune systems are being generated. Immunologists have been using high throughput experimental techniques for a long time, which have generated a vast amount of functional, clinical and epidemiological data. The development of new computational approaches to store and analyse these data are needed.
Recently, immunology-focused resources and software are appearing, which help in understanding the properties of the whole immune system. Immunogenomics, immunoproteomics, epitope prediction and in silico vaccination are different areas of computational immunological research. Recently, Systems Biology approaches have been applied to investigate the properties of the dynamic behaviour of an immune system network. Immunoinformatics includes the study and design of algorithms for mapping potential B- and T-cell epitopes, which lessens the time and cost required for laboratory analysis of pathogen gene products.
Using this information, an immunologist can explore the potential binding sites, which, in turn, leads to the development of new vaccines. Although pathogens grow fast, extraction of their proteins and then testing of those proteins on a large scale is expensive and time consuming.
Immunoinformatics is capable of identifying virulence genes and surface-associated proteins. Figure 1 shows the different research areas of immunoinformatics. All of these areas are described in separate sections of this article. We describe various available information regarding classical immunology, different immunomic databases, and B-cell and T-cell epitope prediction tools and softwares.
Several methods are now available that enable one to map epitopes and design therapeutic vaccines more quickly.
Some of them are described in this article, which concludes with some applications of immunoinformatics.
Immunoinformatics: an integrated scenario
SuperHapten SuperHapten is a manually curated hapten database integrating information from literature and web resources. The commercial availability is documented for about 6, haptens and related antibodies, enabling experimental approaches on cross-reactivity. The haptens are classified regarding their origin: pesticides, herbicides, insecticides, drugs, natural compounds, etc. Queries allow identification of haptens and associated antibodies according to functional class, carrier protein, chemical scaffold, composition or structural similarity.
Methods Mol Biol. Immunoinformatics: a brief review. A large volume of data relevant to immunology research has accumulated due to sequencing of genomes of the human and other model organisms. At the same time, huge amounts of clinical and epidemiologic data are being deposited in various scientific literature and clinical records. This accumulation of the information is like a goldmine for researchers looking for mechanisms of immune function and disease pathogenesis.