Biblio

Found 29 results
Filters: Author is Huang, D.  [Clear All Filters]
2019
Li Y., Bedi R.K, Wiedmer L., Huang D., Śledź P., Caflisch A..  2019.  Flexible binding of m6A reader protein YTHDC1 to its preferred RNA motif. Journal of Chemical Theory and Computation. 15(12):7004-7014.
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.
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.
2014
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.
2013
Steiner S., Magno A., Huang D., Caflisch A..  2013.  Does bromodomain flexibility influence histone recognition? FEBS Letters. 587(14):2158-2163.
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.
2012
Zhao H., Huang D., Caflisch A..  2012.  Discovery of tyrosine kinase inhibitors by docking into an inactive kinase conformation generated by molecular dynamics. ChemMedChem. 7(11):1983-1990.
Huang D., Caflisch A..  2012.  How does Darunavir prevent HIV-1 protease dimerization? Journal of Chemical Theory and Computation. 8(5):1786-1794.
2011
Huang D., Caflisch A..  2011.  The free energy landscape of small molecule unbinding. PLoS Computational Biology. 7(2):e1002002.
Zhao H., Huang D..  2011.  Hydrogen bonding penalty upon ligand binding. PLoS One. 6(6):e19923.
Huang D., Caflisch A..  2011.  Small molecule binding to proteins: Affinity and binding/unbinding dynamics from atomistic simulations. ChemMedChem. 6(9):1578-80.
2010
Huang D., Zhou T., Lafleur K., Nevado C., Caflisch A..  2010.  Kinase selectivity potential for inhibitors targeting the ATP binding site: A network analysis. Bioinformatics. 26(2):198-204.
Huang D., Caflisch A..  2010.  Library screening by fragment-based docking. Journal of Molecular Recognition. 23(2):183-193.
Messner S., Altmeyer M., Zhao H., Pozivil A., Roschitzki B., Gehrig P., Rutishauser D., Huang D., Caflisch A., Hottiger M.O.  2010.  PARP1 ADP-ribosylates lysine residues of the core histone tails. Nucleic Acids Research. 38(19):6350-6362.
Zhou T., Huang D., Caflisch A..  2010.  Quantum mechanical methods for drug design. Current Topics in Medicinal Chemistry. 10(1):33-45.
2009
Ekonomiuk D., Su X.-C., Ozawa K., Bodenreider C., Lim S.P, Yin Z., Keller T.H, Beer D., Patel V., Otting G. et al..  2009.  Discovery of a non-peptidic inhibitor of west nile virus NS3 protease by high-throughput docking. PLoS Neglected Tropical Diseases. 3(1):e356.
Ekonomiuk D., Su X.-C., Ozawa K., Bodenreider C., Lim S.P, Otting G., Huang D., Caflisch A..  2009.  Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics. Journal of Medicinal Chemistry. 52(15):4860-4868.
Bodenreider C., Beer D., Keller T.H, Sonntag S., Wen D., Yap L., Yau Y.H, Shochat S.G, Huang D., Zhou T. et al..  2009.  A fluorescence quenching assay to discriminate between specific and nonspecific inhibitors of dengue virus protease. Analytical Biochemistry. 395(2):195-204.
Su X.-C., Ozawa K., Yagi H., Lim S.P, Wen D., Ekonomiuk D., Huang D., Keller T.H, Sonntag S., Caflisch A. et al..  2009.  NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease. FEBS Journal. 276(15):4244-4255.
Lafleur K., Huang D., Zhou T., Caflisch A., Nevado C..  2009.  Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4). Journal of Medicinal Chemistry. 52(20):6433-6446.
2008
Kolb P., Huang D., Dey F., Caflisch A..  2008.  Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model. Journal of Medicinal Chemistry. 51(5):1179-1188.
Zhou T., Huang D., Caflisch A..  2008.  Is quantum mechanics necessary for predicting binding free energy? Journal of Medicinal Chemistry. 51(14):4280-4288.
Kolb P., Kipouros C.B, Huang D., Caflisch A..  2008.  Structure-based tailoring of compound libraries for high-throughput screening: Discovery of novel EphB4 kinase inhibitors. Proteins: Structure, Function, and Bioinformatics. 73(1):11-18.

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