Immunological Bioinformatics

Structure Evaluation of IroN for Designing a Vaccine against Escherichia Coli, an In Silico Approach

Introduction: Some strains of Escherichia Coli, including intestinal pathogenic strains, commensal strains, and extra intestinal pathogenic E. coli (ExPEC) have a significant impact on human health status. A standard vaccine designed based on conserved epitopes can stimulate a protective immune response against these pathogens. Additionally, enhanced expression at the infection site as a pathog...

Ole Lund Morten Nielsen Claus Lundegaard Can Keşmir Søren Brunak Immunological Bioinformatics

EpiToolKit—a web-based workbench for vaccine design

UNLABELLED EpiToolKit is a virtual workbench for immunological questions with a focus on vaccine design. It offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction, epitope selection for vaccine design, and epitope assembly. In its recently re-implemented version 2.0, EpiToolKit provides a range of new functionality and for the first time allows co...

AntigenMap 3D: an online antigenic cartography resource

SUMMARY Antigenic cartography is a useful technique to visualize and minimize errors in immunological data by projecting antigens to 2D or 3D cartography. However, a 2D cartography may not be sufficient to capture the antigenic relationship from high-dimensional immunological data. AntigenMap 3D presents an online, interactive, and robust 3D antigenic cartography construction and visualization ...

FRED 2: an immunoinformatics framework for Python

UNLABELLED Immunoinformatics approaches are widely used in a variety of applications from basic immunological to applied biomedical research. Complex data integration is inevitable in immunological research and usually requires comprehensive pipelines including multiple tools and data sources. Non-standard input and output formats of immunoinformatics tools make the development of such applicat...