Publications of the Caflisch Group

ZORA Publication List

Publications

• 2019

  • Wiedmer, L., Schärer, C., Spiliotopoulos, D., Hürzeler, M., Śledź, P., & Caflisch, A. (2019). Ligand retargeting by binding site analogy European Journal of Medicinal Chemistry, 175, 107–113. https://doi.org/10.1016/j.ejmech.2019.04.037
  • Garolini, D., Vitalis, A., & Caflisch, A. (2019). Unsupervised identification of states from voltage recordings of neural networks Journal of Neuroscience Methods, 318, 104–117. https://doi.org/10.1016/j.jneumeth.2019.01.019
  • Ilie, I. M., & Caflisch, A. (2019). Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates Chemical Reviews, 119, 6956–6993. https://doi.org/10.1021/acs.chemrev.8b00731
  • Bacci, M., Caflisch, A., & Vitalis, A. (2019). On the removal of initial state bias from simulation data Journal of Chemical Physics, 150, 104105. https://doi.org/10.1063/1.5063556
  • Wiedmer, L., Eberle, S. A., Bedi, R. K., Śledź, P., & Caflisch, A. (2019). A Reader-Based Assay for mA Writers and Erasers Analytical Chemistry, 91, 3078–3084. https://doi.org/10.1021/acs.analchem.8b05500
  • Gay, J. C., Eckenroth, B. E., Evans, C. M., Langini, C., Carlson, S., Lloyd, J. T., Caflisch, A., & Glass, K. C. (2019). Disulfide bridge formation influences ligand recognition by the ATAD2 bromodomain Proteins, 87, 157–167. https://doi.org/10.1002/prot.25636

• 2018

  • Śledź, P., & Caflisch, A. (2018). Protein structure-based drug design: from docking to molecular dynamics Current Opinion in Structural Biology, 48, 93–102. https://doi.org/10.1016/j.sbi.2017.10.010
  • Saponara, E., Visentin, M., Baschieri, F., Seleznik, G., Martinelli, P., Esposito, I., Buschmann, J., Chen, R., Parrotta, R., Borgeaud, N., Bombardo, M., Malagola, E., Caflisch, A., Farhan, H., Graf, R., & Sonda, S. (2018). Serotonin uptake is required for Rac1 activation in Kras-induced acinar-to-ductal metaplasia in the pancreas Journal of Pathology, 246, 352–365. https://doi.org/10.1002/path.5147
  • Zhu, J., Dong, J., Batiste, L., Unzue, A., Dolbois, A., Pascanu, V., Śledź, P., Nevado, C., & Caflisch, A. (2018). Binding Motifs in the CBP Bromodomain: An Analysis of 20 Crystal Structures of Complexes with Small Molecules ACS Medicinal Chemistry Letters, 9, 929–934. https://doi.org/10.1021/acsmedchemlett.8b00286
  • Dalle Vedove, A., Spiliotopoulos, D., D’Agostino, V. G., Marchand, J.-R., Unzue, A., Nevado, C., Lolli, G., & Caflisch, A. (2018). Structural Analysis of Small-Molecule Binding to the BAZ2A and BAZ2B Bromodomains ChemMedChem, 13, 1479–1487. https://doi.org/10.1002/cmdc.201800234
  • Ilie, I. M., & Caflisch, A. (2018). Disorder at the Tips of a Disease-Relevant Aβ42 Amyloid Fibril: A Molecular Dynamics Study Journal of Physical Chemistry B, 122, 11072–11082. https://doi.org/10.1021/acs.jpcb.8b05236
  • Marchand, J.-R., & Caflisch, A. (2018). In silico fragment-based drug design with SEED European Journal of Medicinal Chemistry, 156, 907–917. https://doi.org/10.1016/j.ejmech.2018.07.042
  • Zhu, J., Zhou, C., & Caflisch, A. (2018). Structure-based discovery of selective BRPF1 bromodomain inhibitors European Journal of Medicinal Chemistry, 155, 337–352. https://doi.org/10.1016/j.ejmech.2018.05.037
  • Batiste, L., Unzue, A., Dolbois, A., Hassler, F., Wang, X., Deerain, N., Zhu, J., Spiliotopoulos, D., Nevado, C., & Caflisch, A. (2018). Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple) ACS Central Science, 4, 180–188. https://doi.org/10.1021/acscentsci.7b00401
  • Caflisch, A., & Gianni, S. (2018). Editorial overview: Folding and binding: In silico, in vitro and in cellula Current Opinion in Structural Biology, 48, iv–vii. https://doi.org/10.1016/j.sbi.2018.01.014

• 2017

  • Bacci, M., Langini, C., Vymětal, J., Caflisch, A., & Vitalis, A. (2017). Focused conformational sampling in proteins Journal of Chemical Physics, 147, 195102. https://doi.org/10.1063/1.4996879
  • Langini, C., Caflisch, A., & Vitalis, A. (2017). Correction to: The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes Journal of Biological Chemistry, 292, 19121. https://doi.org/10.1074/jbc.AAC117.000630
  • Abplanalp, J., Leutert, M., Frugier, E., Nowak, K., Feurer, R., Kato, J., Kistemaker, H. V. A., Filippov, D. V., Moss, J., Caflisch, A., & Hottiger, M. O. (2017). Proteomic analyses identify ARH3 as a serine mono-ADP-ribosylhydrolase Nature Communications, 8, 2055. https://doi.org/10.1038/s41467-017-02253-1
  • Marchand, J.-R., Dalle Vedove, A., Lolli, G., & Caflisch, A. (2017). Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking Journal of Chemical Information and Modeling, 57, 2584–2597. https://doi.org/10.1021/acs.jcim.7b00336
  • Spiliotopoulos, D., Wamhoff, E.-C., Lolli, G., Rademacher, C., & Caflisch, A. (2017). Discovery of BAZ2A bromodomain ligands European Journal of Medicinal Chemistry, 139, 564–572. https://doi.org/10.1016/j.ejmech.2017.08.028

Pagination