Journal ArticleDOI
Designing immunogenic peptides
TLDR
Peptides fulfill many roles in immunology, yet none are more important than their role as immunogenic epitopes driving the adaptive immune response, the authors' ultimate bulwark against infectious disease.Abstract:
Peptides fulfill many roles in immunology, yet none are more important than their role as immunogenic epitopes driving the adaptive immune response, our ultimate bulwark against infectious disease. Peptide epitopes are mediated primarily by their interaction with major histocompatibility complexes (T-cell epitopes) and antibodies (B-cell epitopes). As pathogen genomes continue to be revealed, both experimental and computational epitope mapping are becoming crucial tools in vaccine discovery1,2. Immunoinformatics offers many tools, techniques and approaches for in silico epitope characterization, which is capable of greatly accelerating epitope design.read more
Citations
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Journal ArticleDOI
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.
Fabio Sterpone,Simone Melchionna,Pierre Tufféry,Samuela Pasquali,Normand Mousseau,Tristan Cragnolini,Yassmine Chebaro,Jean-François St-Pierre,Maria Kalimeri,Alessandro Barducci,Yoann Laurin,Alex Tek,Marc Baaden,Phuong H. Nguyen,Philippe Derreumaux,Philippe Derreumaux +15 more
TL;DR: The current state of the OPEP coarse-grained protein model and the most exciting applications using advanced conformational sampling methods are reviewed and a perspective on the ongoing developments is presented.
Journal ArticleDOI
Towards high-throughput immunomics for infectious diseases: use of next-generation peptide microarrays for rapid discovery and mapping of antigenic determinants
Santiago J. Carmona,Morten Nielsen,Morten Nielsen,Claus Schafer-Nielsen,Juan Mucci,Jaime Altcheh,Virginia Balouz,Valeria Tekiel,Alberto C.C. Frasch,Oscar Campetella,Carlos A. Buscaglia,Fernán Agüero +11 more
TL;DR: The power of high-density peptide chips for the discovery of pathogen-specific linear B-cell epitopes from clinical samples are shown, setting the stage for high-throughput biomarker discovery screenings and proteome-wide studies of immune responses against pathogens.
Journal ArticleDOI
Peptide-based immunotherapeutics and vaccines.
TL;DR: This special issue on peptide-based vaccines has incorporated 9 original articles and two reviews that deal with and examine various aspects of peptides-based vaccine design.
Journal ArticleDOI
Peptides and peptidomimetics as immunomodulators
TL;DR: The design of peptides/peptidomimetics for immunomodulation in autoimmune diseases and cancer is reviewed and peptide epitopes are used in such a way that the body is trained to recognize and fight the cancer cells locally as well as systemically.
Journal ArticleDOI
Mapping Putative B-Cell Zika Virus NS1 Epitopes Provides Molecular Basis for Anti-NS1 Antibody Discrimination between Zika and Dengue Viruses
Marjorie C. L. C. Freire,Laercio Pol-Fachin,Laercio Pol-Fachin,Danilo F. Coêlho,Danilo F. Coêlho,Isabelle F. T. Viana,Tereza Magalhaes,Marli Tenório Cordeiro,Nico Fischer,Nico Fischer,Felix F. Loeffler,Felix F. Loeffler,Thomas Jaenisch,Thomas Jaenisch,Rafael F. O. França,Ernesto T. A. Marques,Ernesto T. A. Marques,Roberto D. Lins,Roberto D. Lins +18 more
TL;DR: Results provide the molecular basis of differential discrimination between Zika and DENVs by NS1 monoclonal antibodies and suggest that strategies for differential diagnostics on the basis of short linear NS1 sequences are likely to fail due to immunological cross-reactions.
References
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Journal ArticleDOI
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11
TL;DR: The training method underlying the server is the best available, and has been used to predict possible MHC-binding peptides in a series of pathogen viral proteomes including SARS, Influenza and HIV, resulting in an average of 75–80% confirmed MHC binders.
Journal ArticleDOI
HLA class I supertypes: a revised and updated classification
TL;DR: An updated classification of HLA-A and -B class I alleles into supertypes is provided, allowing others to utilize the classification approach going forward and to facilitate epitope identification and vaccine design studies, as well as investigations into disease association and correlates of immunity.
Journal ArticleDOI
T-cell epitope vaccine design by immunoinformatics
TL;DR: Different sequence- and structure-based immunoinformatics methods are reviewed in the paper and the increased understanding of antigen recognition at molecular level has resulted in the development of rationally designed peptide vaccines.
Journal ArticleDOI
Benchmarking B cell epitope prediction: underperformance of existing methods
Martin J Blythe,Darren R. Flower +1 more
TL;DR: This work assesses 484 amino acid propensity scales in combination with ranges of plotting parameters to examine exhaustively the correlation of peaks and epitope location within 50 proteins mapped for polyclonal responses and confirms the null hypothesis.
Journal ArticleDOI
A community resource benchmarking predictions of peptide binding to MHC-I molecules.
Bjoern Peters,Huynh-Hoa Bui,Sune Frankild,Morten Nielsen,Claus Lundegaard,Emrah Kostem,Derek Basch,Kasper Lamberth,Mikkel Harndahl,Ward Fleri,Stephen S. Wilson,John Sidney,Ole Lund,Søren Buus,Alessandro Sette +14 more
TL;DR: A large set of 48,828 quantitative peptide-binding affinity measurements relating to 48 different mouse, human, macaque, and chimpanzee MHC class I alleles is made public to provide a transparent prediction evaluation allowing bioinformaticians to identify promising features of prediction methods and providing guidance to immunologists regarding the reliability of prediction tools.
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An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction
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Patricio Oyarzún,Bostjan Kobe +1 more