scholarly journals Immunoinformatics: Predicting Peptide–MHC Binding

2020 ◽  
Vol 3 (1) ◽  
pp. 191-215 ◽  
Author(s):  
Morten Nielsen ◽  
Massimo Andreatta ◽  
Bjoern Peters ◽  
Søren Buus

Immunoinformatics is a discipline that applies methods of computer science to study and model the immune system. A fundamental question addressed by immunoinformatics is how to understand the rules of antigen presentation by MHC molecules to T cells, a process that is central to adaptive immune responses to infections and cancer. In the modern era of personalized medicine, the ability to model and predict which antigens can be presented by MHC is key to manipulating the immune system and designing strategies for therapeutic intervention. Since the MHC is both polygenic and extremely polymorphic, each individual possesses a personalized set of MHC molecules with different peptide-binding specificities, and collectively they present a unique individualized peptide imprint of the ongoing protein metabolism. Mapping all MHC allotypes is an enormous undertaking that cannot be achieved without a strong bioinformatics component. Computational tools for the prediction of peptide–MHC binding have thus become essential in most pipelines for T cell epitope discovery and an inescapable component of vaccine and cancer research. Here, we describe the development of several such tools, from pioneering efforts to the current state-of-the-art methods, that have allowed for accurate predictions of peptide binding of all MHC molecules, even including those that have not yet been characterized experimentally.

2011 ◽  
Vol 10 (12) ◽  
pp. 733-743 ◽  
Author(s):  
Evelyn Peelen ◽  
Stephanie Knippenberg ◽  
Anne-Hilde Muris ◽  
Mariëlle Thewissen ◽  
Joost Smolders ◽  
...  

2011 ◽  
pp. 2152-2174
Author(s):  
Tao Gong

Static Web immune system is an important applicatiion of artificial immune system, and it is also a good platform to develop new immune computing techniques. On the Static Web system, a normal model is proposed with the space property and the time property of each component, in order to identify the normal state of the system that the artificial immune system protects. Based on the normal model, the Static Web immune sytsem is modelled with three tiers, that is the innate immune tier, the adaptive immune tier and the parallel immune tier. All the three tiers are inspired from the natural immune system. On the tri-tier immune model, the self detection mechanism is proposed and programmed based on the normal model, and the non-self detection is based on the self detection. Besides, the recognition of known non-selfs and unknown non-selfs are designed and analyzed. It is showed that the Static Web immune system is effective and useful for both theory and applications.


Author(s):  
Tao Gong

Static Web immune system is an important applicatiion of artificial immune system, and it is also a good platform to develop new immune computing techniques. On the Static Web system, a normal model is proposed with the space property and the time property of each component, in order to identify the normal state of the system that the artificial immune system protects. Based on the normal model, the Static Web immune sytsem is modelled with three tiers, that is the innate immune tier, the adaptive immune tier and the parallel immune tier. All the three tiers are inspired from the natural immune system. On the tri-tier immune model, the self detection mechanism is proposed and programmed based on the normal model, and the non-self detection is based on the self detection. Besides, the recognition of known non-selfs and unknown non-selfs are designed and analyzed. It is showed that the Static Web immune system is effective and useful for both theory and applications.


2021 ◽  
Vol 7 ◽  
Author(s):  
J. Lacy Kamm ◽  
Christopher B. Riley ◽  
Natalie Parlane ◽  
Erica K Gee ◽  
C. Wayne McIlwraith

Despite significant immunosuppressive activity, allogeneic mesenchymal stromal cells (MSCs) carry an inherent risk of immune rejection when transferred into a recipient. In naïve recipients, this immune response is initially driven by the innate immune system, an immediate reaction to the foreign cells, and later, the adaptive immune system, a delayed response that causes cell death due to recognition of specific alloantigens by host cells and antibodies. This review describes the actions of MSCs to both suppress and activate the different arms of the immune system. We then review the survival and effectiveness of the currently used allogeneic MSC treatments.


Author(s):  
Paul Klenerman

How does the immune system respond to such diverse threats, including viruses never encountered previously by us as a species? The inherent diversity in the immune system can be explained by examining how the adaptive immune system is built, in particular the receptors on B and T lymphocytes. ‘The adaptive immune system: a voyage of (non-)self-discovery’ describes B and T cells, receptors, and the creation of antibodies. Antibody genes are not created as a single unit but are made up from smaller parts, generating many more possible combinations. The antibodies that are created from the genetic template are further honed, becoming highly specific to their target.


2016 ◽  
Vol 2016 ◽  
pp. 1-14 ◽  
Author(s):  
Sara Gabrielli ◽  
Claudio Ortolani ◽  
Genny del Zotto ◽  
Francesca Luchetti ◽  
Barbara Canonico ◽  
...  

Although NK cells are considered part of the innate immune system, a series of evidences has demonstrated that they possess characteristics typical of the adaptive immune system. These NK adaptive features, in particular their memory-like functions, are discussed from an ontogenetic and evolutionary point of view.


2021 ◽  
Vol 5 (1) ◽  
pp. 19-33
Author(s):  
Priyanka Ray ◽  
Noor Haideri ◽  
Inamul Haque ◽  
Omar Mohammed ◽  
Saborni Chakraborty ◽  
...  

Since the early days marking the first use of nanomedicine in the early 80s, there has been a meaningful change in the scientific field involving the Fabrication, characterization, and application of nanomaterials to treat many diseases, including cancers and genetic disorders. As unique and attractive properties of this novel class of materials unraveled, significant advances and discoveries were made over time. Addressing several challenges posed by conventional therapy, which were the only available treatment option for ailing patients, nanomedicine provided enhanced benefits, including reduced dosing, improved pharmacokinetics, and superior targeting efficiency. Several such formulations have successfully made their way to clinics and have shown promise in prolonging terminally ill patient populations' survival rates. However, the complex immune system and its various components, including various proteins and surface receptors, have made nanomaterials' journey from benchtop to the bedside a treacherous one. The innate and adaptive immune system interactions with nanomaterials are still under investigation and full of mysteries. This review highlights the various aspects of therapeutic nanocarriers and their current understanding of their immune systems' interactions.


Parasitology ◽  
1999 ◽  
Vol 119 (S1) ◽  
pp. S107-S110 ◽  
Author(s):  
C. Combes ◽  
S. Morand

SUMMARYWe develop the hypothesis that parasites do not invade extreme environments, i.e. hostile hosts, but rather ‘create’ them. We argue that parasites may have driven the evolution of the constitutive and adaptive immune system. This leads to several implications. First, parasites respond to ‘genes to kill’ by ‘genes to survive’ and this triggers an indefinite selection of measures and counter-measures. Second, these revolutionary arms races may lead to local adaptation, in which parasite populations perform better on local hosts. Third, the evolution of the immune system, whose responses are predictable, may allow parasites to specialize, to evade and even to manipulate. Finally we show that the correlations between the increase in the antibody repertoire, the expansion of MHC loci and parasite pressures support our hypothesis that both host complexity and parasite pressures can be invoked to explain the diversity of antibodies, T-receptors and MHC molecules.


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