Infections and vaccinations typically trigger the production of polyclonal antibodies that bind to many different epitopes on the surface of an antigen or pathogen. These epitopes can vary significantly in how they contribute to immunogenicity or protection. We use molecular modeling to predict or model antigen and pathogen structures, interpret epitope mapping data, and engineer novel vaccine antigens that isolate and present neutralizing epitopes.
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Chaudhury, S., D. R. Ripoll, and A. Wallqvist. Structure-based pKa prediction provides a thermodynamic basis for the role of histidines in pH-induced conformational transitions in dengue virus. Biochemistry and Biophysics Reports. 2015; 4:375-385. [PDF]
Bergmann-Leitner, E. S., S. Chaudhury, N. J. Steers, M. Sabato, V. Delvecchio, A. S. Wallqvist, C. F. Ockenhouse, and E. Angov. Computational and experimental validation of B and T-cell epitopes of the in vivo immune response to a novel malarial antigen. PLOS ONE. 2013 August 16; 8(8):e71610. [PDF]