Biblio

Found 293 results
2014
Fu B., Sahakyan A.B, Camilloni C., Tartaglia G.G, Paci E., Caflisch A., Vendruscolo M., Cavalli A..  2014.  ALMOST: An all atom molecular simulation toolkit for protein structure determination. Journal of Computational Chemistry. 35(14):1101-1105.
Zhao H., Gartenmann L., Dong J., Spiliotopoulos D., Caflisch A..  2014.  Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking. Bioorganic & Medicinal Chemistry Letters. 24(11):2493-2496.
Zhao H., Caflisch A..  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.
Vitalis A., Caflisch A..  2014.  Equilibrium sampling approach to the interpretation of electron density maps. Structure. 22(1):156-167.
Pochorovski I., Knehans T., Nettels D., Müller A.M, Schweizer W.B, Caflisch A., Schuler B., Diederich F..  2014.  Experimental and computational study of BODIPY dye-labeled cavitand dynamics. Journal of the American Chemical Society. 136(6):2441-2449.
Pevzner Y., Frugier E., Schalk V., Caflisch A., Woodcock H.L.  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 N., Vitalis A., Caflisch A..  2014.  High-resolution visualisation of the states and pathways sampled in molecular dynamics simulations. Scientific Reports. 4:6264.
Spiliotopoulos D., Caflisch A..  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.
Novinec M., Korenč M., Caflisch A., Ranganathan R., Lenarčič B., Baici A..  2014.  A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods. Nature Communications. 5:3287.
Unzue A., Dong J., Lafleur K., Zhao H., Frugier E., Caflisch A., Nevado C..  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.
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.
Watson R.P, Christen M.T, Ewald C., Bumbak F., Reichen C., Mihajlovic M., Schmidt E., Güntert P., Caflisch A., Plückthun A. et al..  2014.  Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure. Structure. 22(7):985-995.
Huang D., Rossini E., Steiner S., Caflisch A..  2014.  Structured water molecules in the binding site of bromodomains can be displaced by cosolvent. ChemMedChem. 9(3):573-579.
Friedman R., Caflisch A..  2014.  Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: A simulation study. Proteins: Structure, Function, and Bioinformatics. 82(3):399-404.
2013
Attanasio F., Convertino M., Magno A., Caflisch A., Corazza A., Haridas H., Esposito G., Cataldo S., Pignataro B., Milardi D. et al..  2013.  Carnosine inhibits Aβ42 aggregation by perturbing the H-bond network in and around the central hydrophobic cluster. ChemBioChem. 14(5):583-592.
Zhao H., Caflisch A..  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.
Steiner S., Magno A., Huang D., Caflisch A..  2013.  Does bromodomain flexibility influence histone recognition? FEBS Letters. 587(14):2158-2163.
Buchli B., Waldauer S.A, Walser R., Donten M.L, Pfister R., Blöchliger N., Steiner S., Caflisch A., Zerbe O., Hamm P..  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.
Rosenthal F., Feijs K.LH, Frugier E., Bonalli M., Forst A.H, Imhof R., Winkler H.C, Fischer D., Caflisch A., Hassa P.O et al..  2013.  Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases. Nature Structural & Molecular Biology. 20(4):502-507.
Magno A., Steiner S., Caflisch A..  2013.  Mechanism and kinetics of acetyl-lysine binding to bromodomains. Journal of Chemical Theory and Computation. 9(9):4225-4232.
Scherzer-Attali R., Convertino M., Pellarin R., Gazit E., Segal D., Caflisch A..  2013.  Methylations of tryptophan-modified naphthoquinone affect its inhibitory potential toward Aβ aggregation. The Journal of Physical Chemistry B. 117(6):1780-1789.
Kalgin I.V, Caflisch A., Chekmarev S.F, Karplus M..  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. The Journal of Physical Chemistry B. 117(20):6092-6105.
Lafleur K., Dong J., Huang D., Caflisch A., Nevado C..  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.

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