Alfarano, P., Varadamsetty, G., Ewald, C., Parmeggiani, F., Pellarin, R., Zerbe, O., … Caflisch, A. (2012). Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy. Protein Science, 21(9), 1298-1314. https://doi.org/10.1002/pro.2117 (Original work published 2012)
Tartaglia, G. G., & Caflisch, A. (2007). Computational analysis of the S. cerevisiae proteome reveals the function and cellular localization of the least and most amyloidogenic proteins. Proteins: Structure, Function, and Bioinformatics, 68(1), 273-278. https://doi.org/10.1002/prot.21427 (Original work published)
Cecchini, M., Curcio, R., Pappalardo, M., Melki, R., & Caflisch, A. (2006). A molecular dynamics approach to the structural characterization of amyloid aggregation. Journal of Molecular Biology, 357(4), 1306-1321. https://doi.org/10.1016/j.jmb.2006.01.009 (Original work published)
Gorfe, A. A., Ferrara, P., Caflisch, A., Marti, D. N., Bosshard, H. R., & Jelesarov, I. (2002). Calculation of protein ionization equilibria with conformational sampling: pK<sub>a</sub> of a model leucine zipper, GCN4 and barnase. Proteins: Structure, Function, and Bioinformatics, 46(1), 41-60. https://doi.org/10.1002/prot.10027 (Original work published)
Gsponer, J., Haberthür, U., & Caflisch, A. (2003). The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35. Proceedings of the National Academy of Sciences of the United States of America, 100(9), 5154-5159. https://doi.org/10.1073/pnas.0835307100 (Original work published)