Biblio

Found 80 results
Filters: Keyword is Models, Molecular and Author is Caflisch, A.  [Clear All Filters]
2009
Brooks B.R, Brooks III C.L, Mackerell A.D, Nilsson L., Petrella R.J, Roux B., Won Y., Archontis G., Bartels C., Boresch S. et al..  2009.  CHARMM: The biomolecular simulation program. Journal of Computational Chemistry. 30(10):1545-1614.
Exner V., Aichinger E., Shu H., Wildhaber T., Alfarano P., Caflisch A., Gruissem W., Köhler C., Hennig L..  2009.  The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development. PLoS One. 4(4):e5335.
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.
Muff S., Caflisch A..  2009.  ETNA: Equilibrium transitions network and Arrhenius equation for extracting folding kinetics from REMD simulations. The Journal of Physical Chemistry B. 113(10):3218-3226.
Guarnera E., Pellarin R., Caflisch A..  2009.  How does a simplified-sequence protein fold? Biophys J. 97(6):1737-1746.
Muff S., Caflisch A..  2009.  Identification of the protein folding transition state from molecular dynamics trajectories. Journal of Chemical Physics. 130(12):125104.
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
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.
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.
Friedman R., Caflisch A..  2008.  Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis. Proteins: Structure, Function, and Bioinformatics. 73(4):814-827.
2007
Schroeder V., Vuissoz J.-M., Caflisch A., Kohler H.P.  2007.  Factor XIII activation peptide is released into plasma upon cleavage by thrombin and shows a different structure compared to its bound form. Thrombosis and Haemostasis. 97(6):890-898.
Friedman R., Caflisch A..  2007.  The protonation state of the catalytic aspartates in plasmepsin II. FEBS Letters. 581(21):4120-4124.
Gorfe A.A, Caflisch A..  2007.  Ser170 controls the conformational multiplicity of the loop 166-175 in prion proteins: Implication for conversion and species barrier. FASEB J. 21(12):3279-3287.
Seeber M., Cecchini M., Rao F., Settanni G., Caflisch A..  2007.  Wordom: A program for efficient analysis of molecular dynamics simulations. Bioinformatics. 23(19):2625-2627.
2006
Kolb P., Caflisch A..  2006.  Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking. Journal of Medicinal Chemistry. 49(25):7384-7392.
Huang D., Lüthi U., Kolb P., Cecchini M., Barberis A., Caflisch A..  2006.  In silico discovery of beta-secretase inhibitors. Journal of the American Chemical Society. 128(16):5436-5443.
Cecchini M., Curcio R., Pappalardo M., Melki R., Caflisch A..  2006.  A molecular dynamics approach to the structural characterization of amyloid aggregation. Journal of Molecular Biology. 357(4):1306-1321.
Caflisch A..  2006.  Network and graph analyses of folding free energy surfaces. Current Opinion in Structural Biology. 16(1):71-78.
Seeber M., Fanelli F., Paci E., Caflisch A..  2006.  Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane. Biophysical Journal. 91(9):3276-3284.
Interlandi G., Settanni G., Caflisch A..  2006.  Unfolding transition state and intermediates of the tumor suppressor p16INK4a investigated by molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics. 64(1):178-192.
2005
Curcio R., Caflisch A., Paci E..  2005.  Change of the unbinding mechanism upon a mutation: A molecular dynamics study of an antibody-hapten complex. Protein Science. 14(10):2499-2514.
Huang D., Lüthi U., Kolb P., Edler K., Cecchini M., Audetat S., Barberis A., Caflisch A..  2005.  Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations. Journal of Medicinal Chemistry. 48(16):5108-5111.
Rao F., Settanni G., Guarnera E., Caflisch A..  2005.  Estimation of protein folding probability from equilibrium simulations. Journal of Chemical Physics. 122(18):184901.
Gorfe A.A, Caflisch A..  2005.  Functional plasticity in the substrate binding site of beta-secretase. Structure. 13(10):1487-1498.
Tartaglia G.G, Pellarin R., Cavalli A., Caflisch A..  2005.  Organism complexity anti-correlates with proteomic beta-aggregation propensity. Protein Science. 14(10):2735-2740.

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