Gsponer, J., & Caflisch, A. (2002). Molecular dynamics simulations of protein folding from the transition state. Proceedings of the National Academy of Sciences of the United States of America, 99(10), 6719-6724. https://doi.org/10.1073/pnas.092686399 (Original work published)

Gsponer, J., & Caflisch, A. (2001). Role of native topology investigated by multiple unfolding simulations of four SH3 domains. Journal of Molecular Biology, 309(1), 285-298. https://doi.org/10.1006/jmbi.2001.4552 (Original work published)

Gsponer, J., Ferrara, P., & Caflisch, A. (2001). Flexibility of the murine prion protein and its Asp178Asn mutant investigated by molecular dynamics simulations. Journal of Molecular Graphics and Modelling, 20(2), 169-182. https://doi.org/doi:10.1016/S1093-3263(01)00117-6 (Original work published 2001)

Hiltpold, A., Ferrara, P., Gsponer, J., & Caflisch, A. (2000). Free energy surface of the helical peptide Y(MEARA)₆ The Journal of Physical Chemistry B, 104(43), 10080-10086. https://doi.org/10.1021/jp002207k

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)

Settanni, G., Gsponer, J., & Caflisch, A. (2004). Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations. Biophysical Journal, 86(3), 1691-1701. https://doi.org/10.1016/S0006-3495(04)74238-1 (Original work published 2004)