Applied Bioinformatics Group


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Immunomics

Computational methods are indispensable in vaccine design. Several aspects of computational immunomics are targeted in our group. As results of our research we provide services for the prediction of MHC binding and the antigen processing pathway, as well as for the optimization of epitope-based vaccines.

Computational immunomics applies bioinformatics methods to gain a deeper understanding of the immune system. Furthermore it assists medical research by providing computational models which help to solve immunology-related problems. In our group several aspects of computational immunomics are covered. Our research is supported by the SFB685 grant "Immuntherapie: Von den molekularen Grundlagen zur klinischen Anwendung".

 

Epitope Discovery

We develop methods to predict binding of peptides to MHC class I and MHC class II molecules. This includes the development and integration of methods for modelling all steps of the antigen processing pathway for MHC class I. Our methods are mainly SVM-based and use sequence as well as structural information.
Our webserver EpiToolKit provides a collection of methods from computational immunology for the prediction of MHC ligands or potential T-cell epitopes.

 

Vaccine Design

Our vaccine design framework uses integer linear programming to find a provably optimal set of epitopes for an epitope-based vaccine. Given a set of predicted or experimentally determined epitopes, the mathematical framework efficiently identifies the set most likely to elicit a broad and potent immune response in the target population. With OptiTope, we provide an easy-to-use webserver based on a specific application of this vaccine design framework.

 

Molecular Modeling

We are also developing methods for the structural modeling of proteins relevant to the immune system. A current focus of our work is the automated modeling of the ternary MHC-peptide-TCR complex.

People working in this area

Linus Backert, Christopher Mohr, Benjamin SchubertAndras Szolek, Mathias Walzer

Selected recent publications