Giordano, D., Langini, C., Caflisch, A., Marabotti, A., & Facchiano, A. (2022). Molecular dynamics analysis of the structural properties of the transglutaminases of Kutzneria albida and Streptomyces mobaraensis. Computational and Structural Biotechnology Journal, 20, 3924-3934. https://doi.org/https://doi.org/10.1016/j.csbj.2022.07.024

Ganesan, R., Jelaković, S., Mittl, P. R. E., Caflisch, A., & Grütter, M. G. (2011). In silico identification and crystal structure validation of caspase-3 inhibitors without a P1 aspartic acid moiety. Acta Crystallographica Section F Structural Biology and Crystallization Communications, 67(Pt 8), 842-850. https://doi.org/10.1107/S1744309111018604 (Original work published)

Zhou, T., Huang, D., & Caflisch, A. (2010). Quantum mechanical methods for drug design. Current Topics in Medicinal Chemistry, 10(1), 33-45. https://doi.org/10.2174/156802610790232242 (Original work published 2010)

Huang, D., Zhou, T., Lafleur, K., Nevado, C., & Caflisch, A. (2010). Kinase selectivity potential for inhibitors targeting the ATP binding site: A network analysis. Bioinformatics, 26(2), 198-204. https://doi.org/10.1093/bioinformatics/btp650 (Original work published)

Lafleur, K., Huang, D., Zhou, T., Caflisch, A., & Nevado, C. (2009). Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4). Journal of Medicinal Chemistry, 52(20), 6433-6446. https://doi.org/10.1021/jm9009444 (Original work published)

Brooks, B. R., Brooks III, C. L., Mackerell, A. D., Nilsson, L., Petrella, R. J., Roux, B., … Karplus, M. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30(10), 1545-1614. https://doi.org/10.1002/jcc.21287 (Original work published)

Muff, S., & Caflisch, A. (2009). ETNA: Equilibrium transitions network and Arrhenius equation for extracting folding kinetics from REMD simulations. The Journal of Physical Chemistry B, 113(10), 3218-3226. https://doi.org/10.1021/jp807261h (Original work published)

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)

Caflisch, A. (2006). Network and graph analyses of folding free energy surfaces. Current Opinion in Structural Biology, 16(1), 71-78. https://doi.org/10.1016/j.sbi.2006.01.002 (Original work published 2006)

Taufer, M., Perathoner, E., Cavalli, A., Caflisch, A., & Stricker, T. (2002). Performance characterization of a molecular dynamics code on PC clusters: Is there any easy parallelism in CHARMM? Parallel and Distributed Processing Symposium, Proceedings International (IPDPS 2002). Presented at the. Ft. Lauderdale, FL: IEEE. https://doi.org/10.1109/IPDPS.2002.1015505