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.
Ripoll, D. R., D. A. J. Mitchell, L. C. Dupuy, A. Wallqvist, C. Schmaljohn, and S. Chaudhury. Combinatorial peptide-based epitope mapping from Ebola virus DNA vaccines and infections reveals residue-level determinants of antibody binding. Human Vaccines & Immunotherapeutics. 2017 December 2; 13(12):2953-2966. [PDF]
Mitchell, D. A. J., L. C. Dupuy, M. Sanchez-Lockhart, G. Palacios, J. W. Back, K. Shimanovskaya, S. Chaudhury, D. R. Ripoll, A. Wallqvist, and C. S. Schmaljohn. Epitope mapping of Ebola virus dominant and subdominant glycoprotein epitopes facilitates construction of an epitope-based DNA vaccine able to focus the antibody response in mice. Human Vaccines & Immunotherapeutics. 2017 December 2; 13(12):2883-2893. [PDF]
Chaudhury, S., G. D. Gromowski, D. R. Ripoll, I. V. Khavrutskii, V. Desai, and A. Wallqvist. Dengue virus antibody database: systematically linking serotype-specificity with epitope mapping in dengue virus. PLOS Neglected Tropical Diseases. 2017 February 21; 11(2):e0005395. [PDF]
Ripoll, D. R., I. Khavrutskii, A. Wallqvist, and S. Chaudhury. Modeling the role of epitope arrangement on antibody binding stoichiometry in flaviviruses. Biophysical Journal. 2016 October 18; 111(8):1641-1654. [PDF]
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]