Biblio

Found 53 results
Filters: Author is Caflisch, A. and Keyword is Protein Conformation  [Clear All Filters]
2016
Reichen C., Hansen S., Forzani C., Honegger A., Fleishman S.J, Zhou T., Parmeggiani F., Ernst P., Madhurantakam C., Ewald C. et al..  2016.  Computationally designed armadillo repeat proteins for modular peptide recognition. Journal of Molecular Biology. 428(22):4467-4489.
Lolli G., Caflisch A..  2016.  High-throughput fragment docking into the BAZ2B bromodomain: Efficient in silico screening for X-Ray crystallography. ACS Chemical Biology. 11(3):800-807.
Xu M., Caflisch A., Hamm P..  2016.  Protein structural memory influences ligand binding mode(s) and unbinding rates. Journal of Chemical Theory and Computation. 12(3):1393-1399.
2015
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.
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.
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
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.
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.
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.
Rennebaum S., Caflisch A..  2012.  Inhibition of interdomain motion in g-actin by the natural product latrunculin: A molecular dynamics study. Proteins: Structure, Function, and Bioinformatics. 80(8):1998-2008.
Alfarano P., Varadamsetty G., Ewald C., Parmeggiani F., Pellarin R., Zerbe O., Plückthun A., Caflisch A..  2012.  Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy. Protein Science. 21(9):1298-1314.
Adler-Abramovich L., Vaks L., Carny O., Trudler D., Magno A., Caflisch A., Frenkel D., Gazit E..  2012.  Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylketonuria. Nature Chemical Biology. 8(8):701-706.
2011
Scalco R., Caflisch A..  2011.  Equilibrium distribution from distributed computing (simulations of protein folding). The Journal of Physical Chemistry B. 115(19):6358-6365.
2010
Pellarin R., Schuetz P., Guarnera E., Caflisch A..  2010.  Amyloid fibril polymorphism is under kinetic control. Journal of the American Chemical Society. 132(42):14960-14970.
Schuetz P., Wuttke R., Schuler B., Caflisch A..  2010.  Free energy surfaces from single-distance information. The Journal of Physical Chemistry B. 114(46):15227-15235.
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.
2009
Convertino M., Pellarin R., Catto M., Carotti A., Caflisch A..  2009.  9,10-Anthraquinone hinders beta-aggregation: How does a small molecule interfere with Abeta-peptide amyloid fibrillation? Protein Science. 18(4):792-800.
Ekonomiuk D., Caflisch A..  2009.  Activation of the West Nile virus NS3 protease: Molecular dynamics evidence for a conformational selection mechanism. Protein Science. 18(5):1003-1111.
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.
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.
2008
Interlandi G., Wetzel S.K, Settanni G., Plückthun A., Caflisch A..  2008.  Characterization and further stabilization of designed ankyrin repeat proteins by combining molecular dynamics simulations and experiments. Journal of Molecular Biology. 375(3):837-854.
Parmeggiani F., Pellarin R., Larsen A.P, Varadamsetty G., Stumpp M.T, Zerbe O., Caflisch A., Plückthun A..  2008.  Designed armadillo repeat proteins as general peptide-binding scaffolds: Consensus design and computational optimization of the hydrophobic core. Journal of Molecular Biology. 376(5):1282-1304.
Schenker P., Alfarano P., Kolb P., Caflisch A., Baici A..  2008.  A double-headed cathepsin B inhibitor devoid of warhead. Protein Science. 17(12):2145-2155.
Haberthür U., Caflisch A..  2008.  FACTS: Fast analytical continuum treatment of solvation. Journal of Computational Chemistry. 29(5):701-715.

Pages