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

Vitalis, A., Parker, D., Radler, F., Vargas-Rosales, P. A., Zhang, Y., Marchand, J.-R., & Caflisch, A. (2025). Parallelized tools for the preparation and curation of large libraries for virtual screening. Journal of Computational Chemistry, 46(7). https://doi.org/10.1002/jcc.70074

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

Widmer, J., Vitalis, A., & Caflisch, A. (2024). On the specificity of the recognition of m6A-RNA by YTH reader domains. The Journal of Biological Chemistry, 300(12), 107998. https://doi.org/10.1016/j.jbc.2024.107998 (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)

Cocina, F., Vitalis, A., & Caflisch, A. (2022). Spiking burstiness and working memory in the human medial temporal lobe. Cerebral Cortex Communications, 3(4), tgac039. https://doi.org/https://doi.org/10.1093/texcom/tgac039 (Original work published 2022)

Ilie, I. M., Bacci, M., Vitalis, A., & Caflisch, A. (2022). Antibody binding modulates the dynamics of the membrane-bound prion protein. Biophysical Journal, 121(14), 2813-2825. https://doi.org/10.1016/j.bpj.2022.06.007 (Original work published)

Cocina, F., Vitalis, A., & Caflisch, A. (2021). Unsupervised methods for detection of neural states: case study of hippocampal-amygdala interactions. ENeuro, 8(6). https://doi.org/10.1523/ENEURO.0484-20.2021 (Original work published 2021)

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)

Marchand, J.-R., Knehans, T., Caflisch, A., & Vitalis, A. (2020). An ABSINTH-based protocol for predicting binding affinities between proteins and small molecules. Journal of Chemical Information and Modeling, 60(10), 5188-5202. https://doi.org/10.1021/acs.jcim.0c00558 (Original work published)