Biblio

Found 304 results
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.
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
Attanasio F., Convertino M., Magno A., Caflisch A., Corazza A., Haridas H., Esposito G., Cataldo S., Pignataro B., Milardi D. et al..  2013.  Carnosine inhibits Aβ42 aggregation by perturbing the H-bond network in and around the central hydrophobic cluster. ChemBioChem. 14(5):583-592.
Zhao H., Caflisch A..  2013.  Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics. Bioorganic & Medicinal Chemistry Letters. 23(20):5721-5726.
Steiner S., Magno A., Huang D., Caflisch A..  2013.  Does bromodomain flexibility influence histone recognition? FEBS Letters. 587(14):2158-2163.
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.
Rosenthal F., Feijs K.LH, Frugier E., Bonalli M., Forst A.H, Imhof R., Winkler H.C, Fischer D., Caflisch A., Hassa P.O et al..  2013.  Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases. Nature Structural & Molecular Biology. 20(4):502-507.
Magno A., Steiner S., Caflisch A..  2013.  Mechanism and kinetics of acetyl-lysine binding to bromodomains. Journal of Chemical Theory and Computation. 9(9):4225-4232.
Scherzer-Attali R., Convertino M., Pellarin R., Gazit E., Segal D., Caflisch A..  2013.  Methylations of tryptophan-modified naphthoquinone affect its inhibitory potential toward Aβ aggregation. The Journal of Physical Chemistry B. 117(6):1780-1789.
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.
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.
Blöchliger N., Vitalis A., Caflisch A..  2013.  A scalable algorithm to order and annotate continuous observations reveals the metastable states visited by dynamical systems. Computer Physics Communications. 184(11):2446-2453.
2012
Vitalis A., Caflisch A..  2012.  50 years of Lifson–Roig models: Application to molecular simulation data. Journal of Chemical Theory and Computation. 8(1):363-373.
Caflisch A., Hamm P..  2012.  Complexity in protein folding: Simulation meets experiment. Current Physical Chemistry. 2(1):4-11.
Zhao H., Dong J., Lafleur K., Nevado C., Caflisch A..  2012.  Discovery of a novel chemotype of tyrosine kinase inhibitors by fragment-based docking and molecular dynamics. ACS Medicinal Chemistry Letters. 3(10):834-838.
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.
Zhou T., Caflisch A..  2012.  Distribution of reciprocal of interatomic distances: A fast structural metric. Journal of Chemical Theory and Computation. 8(8):2930-2937.
Vitalis A., Caflisch A..  2012.  Efficient construction of mesostate networks from molecular dynamics trajectories. Journal of Chemical Theory and Computation. 8(2):1108-1120.
Zhou T., Caflisch A..  2012.  Free energy guided sampling. Journal of Chemical Theory and Computation. 8(6):2134-2140.
Huang D., Caflisch A..  2012.  How does Darunavir prevent HIV-1 protease dimerization? Journal of Chemical Theory and Computation. 8(5):1786-1794.
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.
Magno A., Pellarin R., Caflisch A..  2012.  Mechanisms and kinetics of amyloid aggregation investigated by a phenomenological coarse-grained model. Computational Modeling of Biological Systems: Modeling Macromolecular Assemblies. :191-214.
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.
Steiner S., Caflisch A..  2012.  Peptide binding to the PDZ3 domain by conformational selection. Proteins: Structure, Function, and Bioinformatics. 80(11):2562-2572.
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.

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