Publications Caflisch Group

ZORA Publication List

Publications

• 2015

  • Blöchliger, Nicolas; Caflisch, Amedeo; Vitalis, Andreas (2015). Weighted distance functions improve analysis of high-dimensional data: application to molecular dynamics simulations. Journal of Chemical Theory and Computation, 11(11):5481-5492.
  • Huang, Danzhi; Caflisch, Amedeo (2015). The roles of the conserved tyrosine in the β2-α2 loop of the prion protein. Prion, 9(6):412-419.
  • Herrmann, Uli S; Schütz, Anne K; Shirani, Hamid; Huang, Danzhi; Saban, Dino; Nuvolone, Mario; Li, Bei; Ballmer, Boris; Åslund, Andreas K O; Mason, Jeffrey J; Rushing, Elisabeth; Budka, Herbert; Nystrom, Sofie; Hammarstrom, Per; Böckmann, Anja; Caflisch, Amedeo; Meier, Beat H; Nilsson, K Peter R; Hornemann, Simone; Aguzzi, Adriano (2015). Structure-based drug design identifies polythiophenes as antiprion compounds. Science Translational Medicine, 7(299):299ra123.
  • Marchand, Jean-Rémy; Caflisch, Amedeo (2015). Binding Mode of Acetylated Histones to Bromodomains: Variations on a Common Motif. ChemMedChem, 10(8):1327-1333.
  • Zhao, Hongtao; Caflisch, Amedeo (2015). Current kinase inhibitors cover a tiny fraction of fragment space. Bioorganic & Medicinal Chemistry Letters, 25(11):2372-2376.
  • Blöchliger, Nicolas; Xu, Min; Caflisch, Amedeo (2015). Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges. Biophysical Journal, 108(9):2362-2370.
  • Bacci, Marco; Vitalis, Andreas; Caflisch, Amedeo (2015). A molecular simulation protocol to avoid sampling redundancy and discover new states. BBA - Biochimica et Biophysica Acta, 1850(5):889-902.
  • Ewald, Christina; Christen, Martin T; Watson, Randall P; Mihajlovic, Maja; Zhou, Ting; Honegger, Annemarie; Plückthun, Andreas; Caflisch, Amedeo; Zerbe, Oliver (2015). A combined NMR and computational approach to investigate peptide binding to a designed armadillo repeat protein. Journal of Molecular Biology, 427(10):1916-1933.
  • Huang, Danzhi; Caflisch, Amedeo (2015). Evolutionary conserved Tyr169 stabilizes the β2-α2 loop of the prion protein. Journal of the American Chemical Society, 137(8):2948-2957.
  • Müller, Christian S; Knehans, Tim; Davydov, Dmitri R; Bounds, Patricia L; von Mandach, Ursula; Halpert, James R; Caflisch, Amedeo; Koppenol, Willem H (2015). Concurrent cooperativity and substrate inhibition in the epoxidation of carbamazepine by cytochrome P450 3A4 active site mutants inspired by molecular dynamics simulations. Biochemistry, 54(3):711-721.
  • Dong, Jing; Zhao, Hongtao; Zhou, Ting; Spiliotopoulos, Dimitrios; Rajendran, Chitra; Li, Xiao-Dan; Huang, Danzhi; Caflisch, Amedeo (2015). Structural Analysis of the Binding of Type I, I1/2, and II Inhibitors to Eph Tyrosine Kinases. ACS Medicinal Chemistry Letters, 6(1):79-83.
  • Xu, Min; Unzue, Andrea; Dong, Jing; Spiliotopoulos, Dimitrios; Nevado, Cristina; Caflisch, Amedeo (2015). Discovery of CREBBP bromodomain inhibitors by high-throughput docking and hit optimization guided by molecular dynamics. Journal of Medicinal Chemistry:2487-2491.
  • Zhao, Hongtao; Caflisch, Amedeo (2015). Molecular dynamics in drug design. European journal of medicinal chemistry, 91:4-14.

• 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.

Pagination