Publications of the Caflisch Group

ZORA Publication List

Publications

• 2023

  • Bobrovs, R., Drunka, L., Kanepe, I., Jirgensons, A., Caflisch, A., Salvalaglio, M., & Jaudzems, K. (2023). Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors Journal of Chemical Information and Modeling, 63, 6890–6899. https://doi.org/10.1021/acs.jcim.3c00826
  • Cazzanelli, G., Dalle Vedove, A., Parolin, E., D’Agostino, V. G., Unzue, A., Nevado, C., Caflisch, A., & Lolli, G. (2023). Reevaluation of bromodomain ligands targeting BAZ2A Protein Science, 32, e4752. https://doi.org/10.1002/pro.4752
  • Vargas-Rosales, P. A., D’Addio, A., Zhang, Y., & Caflisch, A. (2023). Disrupting Dimeric β-Amyloid by Electric Fields ACS Physical Chemistry Au, 3, 456–466. https://doi.org/10.1021/acsphyschemau.3c00021
  • Widmer, J., Langini, C., Vitalis, A., & Caflisch, A. (2023). Optimized reaction coordinates for analysis of enhanced sampling Journal of Chemical Physics, 159, 015101. https://doi.org/10.1063/5.0149207
  • Bedi, R. K., Huang, D., Li, Y., & Caflisch, A. (2023). Structure-Based Design of Inhibitors of the m$^{6}$A-RNA Writer Enzyme METTL3 ACS Bio & Med Chem Au, 3, 359–370. https://doi.org/10.1021/acsbiomedchemau.3c00023
  • Ilie, I. M., Ehrhardt, C., Caflisch, A., & Weitz-Schmidt, G. (2023). Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations Journal of Chemical Information and Modeling, 63, 3878–3891. https://doi.org/10.1021/acs.jcim.3c00480
  • Reimann, R. R., Puzio, M., Rosati, A., Emmenegger, M., Schneider, B. L., Valdés, P., Huang, D., Caflisch, A., & Aguzzi, A. (2023). Rapid ex vivo reverse genetics identifies the essential determinants of prion protein toxicity Brain Pathology, 33, e13130. https://doi.org/10.1111/bpa.13130
  • Xiang, Y., Zhai, G., Li, Y., Wang, M., Chen, X., Wang, R., Xie, H., Zhang, W., Ge, G., Zhang, Q., Xu, Y., Caflisch, A., Xu, J., Chen, H., & Chen, L. (2023). Ginkgolic acids inhibit SARS-CoV-2 and its variants by blocking the spike protein/ACE2 interplay International Journal of Biological Macromolecules, 226, 780–792. https://doi.org/10.1016/j.ijbiomac.2022.12.057

• 2022

  • Ilie, I. M., & Caflisch, A. (2022). Antibody binding increases the flexibility of the prion protein BBA - Proteins and Proteomics, 1870, 140827. https://doi.org/10.1016/j.bbapap.2022.140827
  • Dehabadi, M. H., Caflisch, A., Ilie, I. M., & Firouzi, R. (2022). Interactions of Curcumin’s Degradation Products with the Aβ$_{42}$ Dimer: A Computational Study. Journal of Physical Chemistry B, 126, 7627–7637. https://doi.org/10.1021/acs.jpcb.2c05846
  • Vargas-Rosales, P. A., & Caflisch, A. (2022). Domino Effect in Allosteric Signaling of Peptide Binding Journal of Molecular Biology, 434, 167661. https://doi.org/10.1016/j.jmb.2022.167661
  • Nai, F., Nachawati, R., Zálešák, F., Wang, X., Li, Y., & Caflisch, A. (2022). Fragment Ligands of the m$^{6}$A-RNA Reader YTHDF2 ACS Medicinal Chemistry Letters, 13, 1500–1509. https://doi.org/10.1021/acsmedchemlett.2c00303
  • Dalle Vedove, A., Cazzanelli, G., Batiste, L., Marchand, J.-R., Spiliotopoulos, D., Corsi, J., D’Agostino, V. G., Caflisch, A., & Lolli, G. (2022). Identification of a BAZ2A-Bromodomain Hit Compound by Fragment Growing ACS Medicinal Chemistry Letters, 13, 1434–1443. https://doi.org/10.1021/acsmedchemlett.2c00173
  • Ilie, I. M., Bacci, M., Vitalis, A., & Caflisch, A. (2022). Antibody binding modulates the dynamics of the membrane-bound prion protein. Biophysical Journal, 121, 2813–2825. https://doi.org/10.1016/j.bpj.2022.06.007
  • García-Viñuales, S., Ilie, I. M., Santoro, A. M., Romanucci, V., Zarrelli, A., Di Fabio, G., Caflisch, A., & Milardi, D. (2022). Silybins inhibit human IAPP amyloid growth and toxicity through stereospecific interactions BBA - Proteins and Proteomics, 1870, 140772. https://doi.org/10.1016/j.bbapap.2022.140772
  • Nass, K. J., Ilie, I. M., Saller, M. J., Driessen, A. J. M., Caflisch, A., Kammerer, R. A., & Li, X. (2022). The role of the N-terminal amphipathic helix in bacterial YidC: Insights from functional studies, the crystal structure and molecular dynamics simulations Biochimica et Biophysica Acta. Biomembranes, 1864, 183825. https://doi.org/10.1016/j.bbamem.2021.183825
  • Salutari, I., & Caflisch, A. (2022). Dynamics of the Histone Acetyltransferase Lysine-Rich Loop in the Catalytic Core of the CREB-Binding Protein Journal of Chemical Information and Modeling, 62, 1014–1024. https://doi.org/10.1021/acs.jcim.1c01423
  • Cocina, F., Vitalis, A., & Caflisch, A. (2022). Spiking burstiness and working memory in the human medial temporal lobe Cerebral Cortex Communications, 3, tgac039. https://doi.org/10.1093/texcom/tgac039
  • 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/10.1016/j.csbj.2022.07.024
  • Schilling, J., Jost, C., Ilie, I. M., Schnabl, J., Buechi, O., Eapen, R. S., Truffer, R., Caflisch, A., & Forrer, P. (2022). Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs Journal of Biological Chemistry, 298, 101403. https://doi.org/10.1016/j.jbc.2021.101403

Pagination