Publications Caflisch Group

ZORA Publication List

Publications

• 2019

  • Li, Yaozong; Bedi, Rajiv Kumar; Wiedmer, Lars; Huang, Danzhi; Śledź, Pawel; Caflisch, Amedeo (2019). Flexible binding of m$^{6}$A reader protein YTHDC1 to its preferred RNA motif. Journal of Chemical Theory and Computation, 15(12):7004-7014.
  • Wiedmer, Lars; Schärer, Claude; Spiliotopoulos, Dimitrios; Hürzeler, Marianne; Śledź, Paweł; Caflisch, Amedeo (2019). Ligand retargeting by binding site analogy. European journal of medicinal chemistry, 175:107-113.
  • Garolini, Davide; Vitalis, Andreas; Caflisch, Amedeo (2019). Unsupervised identification of states from voltage recordings of neural networks. Journal of Neuroscience Methods, 318:104-117.
  • Ilie, Ioana M; Caflisch, Amedeo (2019). Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chemical Reviews, 119(12):6956-6993.
  • Bacci, Marco; Caflisch, Amedeo; Vitalis, Andreas (2019). On the removal of initial state bias from simulation data. Journal of Chemical Physics, 150(10):104105.
  • Wiedmer, Lars; Eberle, Stefanie Alexandra; Bedi, Rajiv Kumar; Śledź, Paweł; Caflisch, Amedeo (2019). A Reader-Based Assay for mA Writers and Erasers. Analytical Chemistry, 91(4):3078-3084.
  • Gay, Jamie C; Eckenroth, Brian E; Evans, Chiara M; Langini, Cassiano; Carlson, Samuel; Lloyd, Jonathan T; Caflisch, Amedeo; Glass, Karen C (2019). Disulfide bridge formation influences ligand recognition by the ATAD2 bromodomain. Proteins, 87(2):157-167.

• 2018

  • Śledź, Pawel; Caflisch, Amedeo (2018). Protein structure-based drug design: from docking to molecular dynamics. Current Opinion in Structural Biology, 48:93-102.
  • Saponara, Enrica; Visentin, Michele; Baschieri, Francesco; Seleznik, Gitta; Martinelli, Paola; Esposito, Irene; Buschmann, Johanna; Chen, Rong; Parrotta, Rossella; Borgeaud, Nathalie; Bombardo, Marta; Malagola, Ermanno; Caflisch, Amedeo; Farhan, Hesso; Graf, Rolf; Sonda, Sabrina (2018). Serotonin uptake is required for Rac1 activation in Kras-induced acinar-to-ductal metaplasia in the pancreas. Journal of Pathology, 246(3):352-365.
  • Esposito, C; Wiedmer, L; Caflisch, A (2018). In Silico Identification of JMJD3 Demethylase Inhibitors. Journal of Chemical Information and Modeling, 58(10):2151-2163.
  • Zhu, Jian; Dong, Jing; Batiste, Laurent; Unzue, Andrea; Dolbois, Aymeric; Pascanu, Vlad; Śledź, Paweł; Nevado, Cristina; Caflisch, Amedeo (2018). Binding Motifs in the CBP Bromodomain: An Analysis of 20 Crystal Structures of Complexes with Small Molecules. ACS Medicinal Chemistry Letters, 9(9):929-934.
  • Dalle Vedove, Andrea; Spiliotopoulos, Dimitrios; D'Agostino, Vito G; Marchand, Jean-Rémy; Unzue, Andrea; Nevado, Cristina; Lolli, Graziano; Caflisch, Amedeo (2018). Structural Analysis of Small-Molecule Binding to the BAZ2A and BAZ2B Bromodomains. ChemMedChem, 13(14):1479-1487.
  • Ilie, Ioana M; Caflisch, Amedeo (2018). Disorder at the Tips of a Disease-Relevant Aβ42 Amyloid Fibril: A Molecular Dynamics Study. Journal of Physical Chemistry B, 122:11072-11082.
  • Marchand, Jean-Rémy; Caflisch, Amedeo (2018). In silico fragment-based drug design with SEED. European journal of medicinal chemistry, 156:907-917.
  • Zhu, Jian; Zhou, Chunxian; Caflisch, Amedeo (2018). Structure-based discovery of selective BRPF1 bromodomain inhibitors. European journal of medicinal chemistry, 155:337-352.
  • Unzue, A; Cribiú, R; Hoffman, M M; Knehans, T; Lafleur, K; Caflisch, A; Nevado, C (2018). Iriomoteolides: novel chemical tools to study actin dynamics. Chemical Science, 9(15):3793-3802.
  • Batiste, Laurent; Unzue, Andrea; Dolbois, Aymeric; Hassler, Fabrice; Wang, Xuan; Deerain, Nicholas; Zhu, Jian; Spiliotopoulos, Dimitrios; Nevado, Cristina; Caflisch, Amedeo (2018). Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple). ACS Central Science, 4(2):180-188.
  • Caflisch, Amedeo; Gianni, Stefano (2018). Editorial overview: Folding and binding: In silico, in vitro and in cellula. Current Opinion in Structural Biology, 48:iv-vii.

• 2017

  • Bacci, Marco; Langini, Cassiano; Vymětal, Jiří; Caflisch, Amedeo; Vitalis, Andreas (2017). Focused conformational sampling in proteins. Journal of Chemical Physics, 147(19):195102.
  • Langini, Cassiano; Caflisch, Amedeo; Vitalis, Andreas (2017). Correction to: The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes. Journal of Biological Chemistry, 292(46):19121.
  • Abplanalp, Jeannette; Leutert, Mario; Frugier, Emilie; Nowak, Kathrin; Feurer, Roxane; Kato, Jiro; Kistemaker, Hans V A; Filippov, Dmitri V; Moss, Joel; Caflisch, Amedeo; Hottiger, Michael O (2017). Proteomic analyses identify ARH3 as a serine mono-ADP-ribosylhydrolase. Nature Communications, 8(1):2055.
  • Marchand, Jean-Rémy; Dalle Vedove, Andrea; Lolli, Graziano; Caflisch, Amedeo (2017). Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking. Journal of Chemical Information and Modeling, 57(10):2584-2597.
  • Spiliotopoulos, Dimitrios; Wamhoff, Eike-Christian; Lolli, Graziano; Rademacher, Christoph; Caflisch, Amedeo (2017). Discovery of BAZ2A bromodomain ligands. European journal of medicinal chemistry, 139:564-572.
  • Bacci, Marco; Vymětal, Jiří; Mihajlovic, Maja; Caflisch, Amedeo; Vitalis, Andreas (2017). Amyloid β Fibril Elongation by Monomers Involves Disorder at the Tip. Journal of Chemical Theory and Computation, 13(10):5117-5130.
  • Langini, Cassiano; Caflisch, Amedeo; Vitalis, Andreas (2017). The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes. Journal of Biological Chemistry, 292(40):16734-16745.
  • Peón, Antonio; Robles, Adrián; Blanco, Beatriz; Convertino, Marino; Thompson, Paul; Hawkins, Alastair R; Caflisch, Amedeo; González-Bello, Concepción (2017). Reducing the Flexibility of Type II Dehydroquinase for Inhibition: A Fragment-Based Approach and Molecular Dynamics Study. ChemMedChem, 12(18):1512-1524.
  • Spiliotopoulos, Dimitrios; Zhu, Jian; Wamhoff, Eike-Christian; Deerain, Nicholas; Marchand, Jean-Rémy; Aretz, Jonas; Rademacher, Christoph; Caflisch, Amedeo (2017). Virtual screen to NMR (VS2NMR): Discovery of fragment hits for the CBP bromodomain. Bioorganic & Medicinal Chemistry Letters, 27(11):2472-2478.
  • Ghayor, Chafik; Gjoksi, Bebeka; Dong, Jing; Siegenthaler, Barbara; Caflisch, Amedeo; Weber, Franz E (2017). N,N Dimethylacetamide a drug excipient that acts as bromodomain ligand for osteoporosis treatment. Scientific Reports, 7:42108.

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