Biblio

Found 274 results
2015
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.
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.

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