Biblio

Found 256 results
2015
Marchand J.-R., Caflisch A..  2015.  Binding mode of acetylated histones to bromodomains: Variations on a common motif. ChemMedChem. 10(8):1327-1333.
Ewald C., Christen M.T, Watson R.P, Mihajlovic M., Zhou T., Honegger A., Plückthun A., Caflisch A., Zerbe O..  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.
Müller C.S, Knehans T., Davydov D.R, Bounds P.L, von Mandach U., Halpert J.R, Caflisch A., Koppenol W.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.
Zhao H., Caflisch A..  2015.  Current kinase inhibitors cover a tiny fraction of fragment space. Bioorganic & Medicinal Chemistry Letters. 25(11):2372-2376.
Huang D., Caflisch A..  2015.  Evolutionary conserved Tyr169 stabilizes the β2-α2 loop of the prion protein. Journal of the American Chemical Society. 137(8):2948-2957.
Zhao H., Caflisch A..  2015.  Molecular dynamics in drug design. European Journal of Medicinal Chemistry. 91:4-14.
Bacci M., Vitalis A., Caflisch A..  2015.  A molecular simulation protocol to avoid sampling redundancy and discover new states. Biochimica et Biophysica Acta (BBA) - General Subjects. 1850(5):889-902.
Blöchliger N., Xu M., Caflisch A..  2015.  Peptide binding to a PDZ domain by electrostatic steering via nonnative salt bridges. Biophysical Journal. 108(9):2362-2370.
Huang D., Caflisch A..  2015.  The roles of the conserved tyrosine in the β2-α2 loop of the prion protein. Prion. 9(6):412-419.
Dong J., Zhao H., Zhou T., Spiliotopoulos D., Rajendran C., Li X.-D., Huang D., Caflisch A..  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.
Herrmann U.S, Schütz A.K, Shirani H., Huang D., Saban D., Nuvolone M., Li B., Ballmer B., Åslund A.KO, Mason J.J et al..  2015.  Structure-based drug design identifies polythiophenes as antiprion compounds. Science Translational Medicine. 7(299):299ra123.
Blöchliger N., Caflisch A., Vitalis A..  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.
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.

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