Reichen, C., Hansen, S., Forzani, C., Honegger, A., Fleishman, S. J., Zhou, T., … Plückthun, A. (2016). Computationally designed armadillo repeat proteins for modular peptide recognition. Journal of Molecular Biology, 428(22), 4467-4489. https://doi.org/10.1016/j.jmb.2016.09.012 (Original work published)

Lolli, G., & Caflisch, A. (2016). High-throughput fragment docking into the BAZ2B bromodomain: Efficient in silico screening for X-Ray crystallography. ACS Chemical Biology, 11(3), 800-807. https://doi.org/10.1021/acschembio.5b00914 (Original work published)

Huang, D., & Caflisch, A. (2015). The roles of the conserved tyrosine in the β2-α2 loop of the prion protein. Prion, 9(6), 412-419. https://doi.org/10.1080/19336896.2015.1115944

Xu, M., Caflisch, A., & Hamm, P. (2016). Protein structural memory influences ligand binding mode(s) and unbinding rates. Journal of Chemical Theory and Computation, 12(3), 1393-1399. https://doi.org/10.1021/acs.jctc.5b01052 (Original work published)

Fu, B., Sahakyan, A. B., Camilloni, C., Tartaglia, G. G., Paci, E., Caflisch, A., … Cavalli, A. (2014). ALMOST: An all atom molecular simulation toolkit for protein structure determination. Journal of Computational Chemistry, 35(14), 1101-1105. https://doi.org/10.1002/jcc.23588 (Original work published)

Friedman, R., & Caflisch, A. (2014). Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: A simulation study. Proteins: Structure, Function, and Bioinformatics, 82(3), 399-404. https://doi.org/10.1002/prot.24402 (Original work published 2014)

Buchli, B., Waldauer, S. A., Walser, R., Donten, M. L., Pfister, R., Blöchliger, N., … Hamm, P. (2013). Kinetic response of a photoperturbed allosteric protein. Proceedings of the National Academy of Sciences of the United States of America, 110(29), 11725-11730. https://doi.org/10.1073/pnas.1306323110 (Original work published)

Kalgin, I. V., Caflisch, A., Chekmarev, S. F., & Karplus, M. (2013). New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: Application to a hydrodynamic analysis of the folding flow. The Journal of Physical Chemistry B, 117(20), 6092-6105. https://doi.org/10.1021/jp401742y (Original work published)

Zhao, H., Huang, D., & Caflisch, A. (2012). Discovery of tyrosine kinase inhibitors by docking into an inactive kinase conformation generated by molecular dynamics. ChemMedChem, 7(11), 1983-1990. https://doi.org/10.1002/cmdc.201200331 (Original work published 2012)

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)