(External) In silico design of multi-epitope fusion proteins using immunoinformatic tools

Advisor: Dion Lepp, Guelph Research and Development Centre, Agriculture and Agri-Food Canada

Suggested co-advisors: TBD

The proposed project will involve the evaluation and application of various immunoinformatic tools to design multivalent vaccines, which will ultimately be assessed for efficacy in animal vaccination trials. Several different known protein antigens will be analyzed to predict putative epitope regions, which will be selected based on predicted antigenicity, allergenicity and toxicity.  Selected epitopes will be combined with linkers to generate candidate fusion proteins. Protein structure models of the candidate fusion proteins will be generated with AlphaFold3 and evaluated for solubility, stability and epitope accessibility. Finally, expression vectors will be designed for cloning and production of the fusion proteins.  Where possible, the analysis steps will be performed on the Agriculture and Agri-Food Canada General Purpose Science Cluster (GPSC) using  command-line tools, and incorporated into a bioinformatics pipeline for use by other researchers.

This project is suitable for one or two semesters. The student is required to occasionally be on-site.

Knowledge/Skills

• Knowledge of microbiology, molecular biology, immunology and protein structure
• Experience with bash command-line and python programming