Publications of the Caflisch Group

ZORA Publication List

Publications

• 2014

  • Spiliotopoulos, Dimitrios; Caflisch, Amedeo (2014). Molecular Dynamics Simulations of Bromodomains Reveal Binding-Site Flexibility and Multiple Binding Modes of the Natural Ligand Acetyl-Lysine. Israel Journal of Chemistry, 54(8-9):1084-1092.
  • Watson, Randall P; Christen, Martin T; Ewald, Christina; Bumbak, Fabian; Reichen, Christian; Mihajlovic, Maja; Schmidt, Elena; Güntert, Peter; Caflisch, Amedeo; Plückthun, Andreas; Zerbe, Oliver (2014). Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure. Structure, 22(7):985-995.
  • Unzue, Andrea; Dong, Jing; Lafleur, Karine; Zhao, Hongtao; Frugier, Emilie; Caflisch, Amedeo; Nevado, Cristina (2014). Pyrrolo[3,2-b]quinoxaline derivatives as types I1/2 and II Eph tyrosine kinase inhibitors: structure-based design, synthesis, and in vivo validation. Journal of Medicinal Chemistry, 57(15):6834-6844.
  • Pevzner, Yuri; Frugier, Emilie; Schalk, Vinushka; Caflisch, Amedeo; Woodcock, H Lee (2014). Fragment-based docking: Development of the CHARMMing web user interface as a platform for computer-aided drug design. Journal of Chemical Information and Modeling, 54(9):2612-2620.
  • Blöchliger, Nicolas; Vitalis, Andreas; Caflisch, Amedeo (2014). High-resolution visualisation of the states and pathways sampled in molecular dynamics simulations. Scientific Reports, 4(6264):online.
  • Zhao, Hongtao; Gartenmann, Lisa; Dong, Jing; Spiliotopoulos, Dimitrios; Caflisch, Amedeo (2014). Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking. Bioorganic & Medicinal Chemistry Letters, 24(11):2493-2496.
  • Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea (2014). ALMOST: an all atom molecular simulation toolkit for protein structure determination. Journal of Computational Chemistry, 35(14):1101-1105.
  • Zhao, Hongtao; Caflisch, Amedeo (2014). Discovery of dual ZAP70 and Syk kinases inhibitors by docking into a rare C-helix-out conformation of Syk. Bioorganic & Medicinal Chemistry Letters, 24(6):1523-1527.
  • Novinec, Marko; Korenč, Matevž; Caflisch, Amedeo; Ranganathan, Rama; Lenarčič, Brigita; Baici, Antonio (2014). A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods. Nature Communications, 5:3287.
  • Zhou, T; Georgeon, S; Moser, R; Moore, D J; Caflisch, A; Hantschel, O (2014). Specificity and mechanism-of-action of the JAK2 tyrosine kinase inhibitors ruxolitinib and SAR302503 (TG101348). Leukemia, 28(2):404-407.
  • Pochorovski, Igor; Knehans, Tim; Nettels, Daniel; Müller, Astrid M; Schweizer, W Bernd; Caflisch, Amedeo; Schuler, Benjamin; Diederich, François (2014). Experimental and computational study of BODIPY dye-labeled cavitand dynamics. Journal of the American Chemical Society, 136(6):2441-2449.
  • Vitalis, Andreas; Caflisch, Amedeo (2014). Equilibrium sampling approach to the interpretation of electron density maps. Structure, 22(1):156-167.
  • Friedman, Ran; Caflisch, Amedeo (2014). Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: a simulation study. Proteins, 82(3):399-404.

• 2013

  • Huang, Danzhi; Rossini, Emanuele; Steiner, Sandra; Caflisch, Amedeo (2013). Structured water molecules in the binding site of bromodomains can be displaced by cosolvent. ChemMedChem, 9(3):573-579.
  • Magno, Andrea; Steiner, Sandra; Caflisch, Amedeo (2013). Mechanism ad kinetics of acetyl-lysine binding to bromodomains. Journal of Chemical Theory and Computation, 9(9):4225-4232.
  • Blöchliger, Nicolas; Vitalis, Andreas; Caflisch, Amedeo (2013). A scalable algorithm to order ad annotate continuous observations reveals the metastable states visited by dynamical systems. Computer Physics Communications, 184:2446-2453.
  • Zhao, Hongtao; Caflisch, Amedeo (2013). Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics. Bioorganic & Medicinal Chemistry Letters, 23(20):5721-5726.
  • Buchli, Brigitte; Waldauer, Steven A; Walser, Reto; Donten, Mateusz L; Pfister, Rolf; Blöchliger, Nicolas; Steiner, Sandra; Caflisch, Amedeo; Zerbe, Oliver; Hamm, Peter (2013). Kinetic response of a photoperturbed allosteric protein. Proceedings of the National Academy of Sciences of the United States of America, 110(29):11725-11730.
  • Steiner, Sandra; Magno, Andrea; Huang, Danzhi; Caflisch, Amedeo (2013). Does bromodomain flexibility influence histone recognition?. FEBS letters, 587(14):2158-2163.
  • Kalgin, Igor V; Caflisch, Amedeo; Chekmarev, Sergei F; Karplus, Martin (2013). New Insights into the Folding of a β-Sheet Miniprotein in a Reduced Space of Collective Hydrogen Bond Variables: Application to a Hydrodynamic Analysis of the Folding Flow. Journal of Physical Chemistry B, 117(20):6092-6105.
  • Attanasio, Francesco; Convertino, Marino; Magno, Andrea; Caflisch, Amedeo; Corazza, Alessandra; Haridas, Haritha; Esposito, Gennaro; Cataldo, Sebastiano; Pignataro, Bruno; Milardi, Danilo; Rizzarelli, Enrico (2013). Carnosine inhibits Aβ42 aggregation by perturbing the H-Bond network in and around the central Hydrophobic cluster. Chembiochem, 14(5):583-592.
  • Rosenthal, Florian; Feijs, Karla L H; Frugier, Emilie; Bonalli, Mario; Forst, Alexandra H; Imhof, Ralph; Winkler, Hans C; Fischer, David; Caflisch, Amedeo; Hassa, Paul O; Lüscher, Bernhard; Hottiger, Michael O (2013). Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases. Nature Structural & Molecular Biology, 20(4):502-507.
  • Scherzer-Attali, Roni; Convertino, Marino; Pellarin, Riccardo; Gazit, Ehud; Segal, Daniel; Caflisch, Amedeo (2013). Methylations of Tryptophan-Modified Naphthoquinone affect its inhibitory potential toward Aβ aggregation. Journal of Physical Chemistry B, 117(6):1780-1789.
  • Lafleur, Karine; Dong, Jing; Huang, Danzhi; Caflisch, Amedeo; Nevado, Cristina (2013). Optimization of inhibitors of the tyrosine kinase EphB4. 2. Cellular potency improvement and binding mode validation by X-ray crystallography. Journal of Medicinal Chemistry, 56(1):84-96.

• 2012

  • Caflisch, A; Hamm, P (2012). Complexity in Protein Folding: Simulation Meets Experiment. Current Physical Chemistry, 2:4-11.
  • Huang, Danzhi; Caflisch, Amedeo (2012). How Does Darunavir Prevent HIV-1 Protease Dimerization?. Journal of Chemical Theory and Computation, 8(5):1786-1794.
  • Scalco, Riccardo; Caflisch, Amedeo (2012). Ultrametricity in Protein Folding Dynamics. Journal of Chemical Theory and Computation, 8(5):1580-1588.
  • Vitalis, Andreas; Caflisch, Amedeo (2012). Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories. Journal of Chemical Theory and Computation, 8(3):1108-1120.
  • Vitalis, Andreas; Caflisch, Amedeo (2012). 50 Years of Lifson–Roig Models: Application to Molecular Simulation Data. Journal of Chemical Theory and Computation, 8(1):363-373.
  • Steiner, Sandra; Caflisch, Amedeo (2012). Peptide binding to the PDZ3 domain by conformational selection. Proteins, 80(11):2562-2572.
  • Adler-Abramovich, Lihi; Vaks, Lilach; Carny, Ohad; Trudler, Dorit; Magno, Andrea; Caflisch, Amedeo; Frenkel, Dan; Gazit, Ehud (2012). Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylketonuria. Nature Chemical Biology, 8(8):701-706.
  • Rennebaum, Sandra; Caflisch, Amedeo (2012). Inhibition of interdomain motion in g-actin by the natural product latrunculin: a molecular dynamics study. Proteins, 80(8):1998-2008.
  • Waldauer, Steven A; Hassan, Shabir; Paoli, Beatrice; Donaldson, Paul M; Pfister, Rolf; Hamm, Peter; Caflisch, Amedeo; Pellarin, Riccardo (2012). Photocontrol of reversible amyloid formation with a minimal-design peptide. Journal of Physical Chemistry B, 116(30):8961-8973.
  • Alfarano, P; Varadamsetty, G; Ewald, C; Parmeggiani, F; Pellarin, R; Zerbe, O; Plückthun, A; Caflisch, A (2012). Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy. Protein Science, 21(9):1298-1314.

Pagination