Li, Y., Bedi, R. K., Ojeda-May, P., & Caflisch, A. (2026). Recognition loop dynamics differentiates m6A-mRNA reader domains of YTHDF proteins. Journal of Chemical Theory and Computation, 20(22), 10988–11003. https://doi.org/10.1021/acs.jctc.6c01247 (Original work published)

Vitalis, A., Winkler, S., Zhang, Y., Widmer, J., & Caflisch, A. (2025). A FAIR-compliant management solution for molecular simulation trajectories. Journal of Chemical Information and Modeling, 65(5), 2443-2455. https://doi.org/10.1021/acs.jcim.4c01301

Zhang, Y., & Vitalis, A. (2025). Benchmarking the robustness of the correct identification of flexible 3D objects using common machine learning models. Patterns, 6(1), 101147. https://doi.org/https://doi.org/10.1016/j.patter.2024.101147

Vargas-Rosales, P. A., DAddio, A., Zhang, Y., & Caflisch, A. (2023). Disrupting dimeric β-amyloid by electric fields. ACS Physical Chemistry Au, 3(5), 456–466. https://doi.org/10.1021/acsphyschemau.3c00021 (Original work published)

Widmer, J., Langini, C., Vitalis, A., & Caflisch, A. (2023). Optimized reaction coordinates for analysis of enhanced sampling. The Journal of Chemical Physics, 159(1), 015101-24. https://doi.org/10.1063/5.0149207 (Original work published)

Bedi, R. K., Huang, D., Li, Y., & Caflisch, A. (2023). Structure-based design of inhibitors of the m6A‑RNA writer enzyme METTL3. ACS Bio & Med Chem Au, 3(4), 359–370. https://doi.org/10.1021/acsbiomedchemau.3c00023 (Original work published)

Li, Y., Bedi, R. K., Nai, F., von Roten, V., Dolbois, A., Zálešák, F., … Caflisch, A. (2022). Structure-based design of ligands of the m6A-RNA reader YTHDC1. European Journal of Medicinal Chemistry Reports, 5, 100057. https://doi.org/https://doi.org/10.1016/j.ejmcr.2022.100057

Cocina, F., Vitalis, A., & Caflisch, A. (2020). SAPPHIRE-based clustering. Journal of Chemical Theory and Computation, 16(10), 6383–6396. https://doi.org/10.1021/acs.jctc.0c00604 (Original work published)

Caflisch, A. (2020). Kinetic control of amyloidogenesis calls for unconventional drugs to fight Alzheimer’s disease. ACS Chemical Neuroscience, 11(2), 103-104. https://doi.org/10.1021/acschemneuro.9b00676 (Original work published)

Li, Y., Bedi, R. K., Wiedmer, L., Huang, D., Śledź, P., & Caflisch, A. (2019). Flexible binding of m6A reader protein YTHDC1 to its preferred RNA motif. Journal of Chemical Theory and Computation, 15(12), 7004-7014. https://doi.org/10.1021/acs.jctc.9b00987 (Original work published)