Found 269 results
Filters: Author is Caflisch, A.  [Clear All Filters]
Friedman R., Pellarin R., Caflisch A..  2009.  Amyloid aggregation on lipid bilayers and its impact on membrane permeability. J. Mol. Biol.. 387(2):407-415.
Paoli B., Seeber M., Backus E.HG, Ihalainen J.A, Hamm P., Caflisch A..  2009.  Bulky side chains and non-native salt bridges slow down the folding of a cross-linked helical peptide: A combined molecular dynamics and time-resolved infrared spectroscopy study. The Journal of Physical Chemistry B. 113(13):4435-4442.
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.
Zhou T., Caflisch A..  2009.  Data management system for distributed virtual screening. Journal of Chemical Information and Modeling. 49(1):145-152.
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.
Friedman R., Caflisch A..  2009.  Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring. ChemMedChem. 4(8):1317-1326.
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.
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.
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.
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.
Benedix A., Becker C.M, de Groot B.L, Caflisch A., Böckmann R.A.  2009.  Predicting free energy changes using structural ensembles. Nat Methods. 6(1):3-4.
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.
Ihalainen J.A, Paoli B., Muff S., Backus E.HG, Bredenbeck J., Woolley G.A, Caflisch A., Hamm P..  2008.  Alpha-Helix folding in the presence of structural constraints. Proceedings of the National Academy of Sciences of the United States of America. 105(28):9588-9593.
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.
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.
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.
Schuetz P., Caflisch A..  2008.  Efficient modularity optimization by multistep greedy algorithm and vertex mover refinement. Physical Review E: Statistical, Nonlinear, and Soft Matter Physics. 77(4.2):046112.
Haberthür U., Caflisch A..  2008.  FACTS: Fast analytical continuum treatment of solvation. Journal of Computational Chemistry. 29(5):701-715.
Dey F., Caflisch A..  2008.  Fragment-based de novo ligand design by multiobjective evolutionary optimization. Journal of Chemical Information and Modeling. 48(3):679-690.
Muff S., Caflisch A..  2008.  Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein. Proteins: Structure, Function, and Bioinformatics. 70(4):1185-1195.
Schuetz P., Caflisch A..  2008.  Multistep greedy algorithm identifies community structure in real-world and computer-generated networks. Physical Review E: Statistical, Nonlinear, and Soft Matter Physics. 78(2.2):026112.