Biblio

Found 309 results
2012
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.
Waldauer S.A, Hassan S., Paoli B., Donaldson P.M, Pfister R., Hamm P., Caflisch A., Pellarin R..  2012.  Photocontrol of reversible amyloid formation with a minimal-design peptide. The Journal of Physical Chemistry B. 116(30):8961-8973.
Scalco R., Caflisch A..  2012.  Ultrametricity in protein folding dynamics. Journal of Chemical Theory and Computation. 8(5):1580-1588.
2011
Zheng W., Qi B., Rohrdanz M.A, Caflisch A., Dinner A.R, Clementi C..  2011.  Delineation of folding pathways of a β-sheet miniprotein. The Journal of Physical Chemistry B. 115(44):13065-13074.
Convertino M., Vitalis A., Caflisch A..  2011.  Disordered binding of small molecules to Aβ(12-28). The Journal of Biological Chemistry. 286(48):41578-41588.
Mishra S., Caflisch A..  2011.  Dynamics in the active site of β-secretase: A network analysis of atomistic simulations. Biochemistry. 50(43):9328-9339.
Scalco R., Caflisch A..  2011.  Equilibrium distribution from distributed computing (simulations of protein folding). The Journal of Physical Chemistry B. 115(19):6358-6365.
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.
Ganesan R., Jelaković S., Mittl P.RE, Caflisch A., Grütter M.G.  2011.  In silico identification and crystal structure validation of caspase-3 inhibitors without a P1 aspartic acid moiety. Acta Crystallographica Section F Structural Biology and Crystallization Communications. 67(Pt 8):842-850.
Huang D., Caflisch A..  2011.  Small molecule binding to proteins: Affinity and binding/unbinding dynamics from atomistic simulations. ChemMedChem. 6(9):1578-80.
Frydman-Marom A., Convertino M., Pellarin R., Lampel A., Shaltiel-Karyo R., Segal D., Caflisch A., Shalev D.E, Gazit E..  2011.  Structural basis for inhibiting β-amyloid oligomerization by a non-coded β-breaker-substituted endomorphin analogue. ACS Chemical Biology. 6(11):1265-1276.
Friedman R., Caflisch A..  2011.  Surfactant effects on amyloid aggregation kinetics. Journal of Molecular Biology. 414(2):303-312.
Seeber M., Felline A., Raimondi F., Muff S., Friedman R., Rao F., Caflisch A., Fanelli F..  2011.  Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. Journal of Computational Chemistry. 32(6):1183-1194.
2010
Backus E.HG, Bloem R., Donaldson P.M, Ihalainen J.A, Pfister R., Paoli B., Caflisch A., Hamm P..  2010.  2D-IR study of a photoswitchable isotope-labeled alpha-helix. The Journal of Physical Chemistry B. 114(10):3735-3740.
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.
Zhou T., Lafleur K., Caflisch A..  2010.  Complementing ultrafast shape recognition with an optical isomerism descriptor. Journal of Molecular Graphics and Modelling. 29(3):443-449.
Scherzer-Attali R., Pellarin R., Convertino M., Frydman-Marom A., Egoz-Matia N., Peled S., Levy-Sakin M., Shalev D.E, Caflisch A., Gazit E. et al..  2010.  Complete phenotypic recovery of an Alzheimer's disease model by a quinone-tryptophan hybrid aggregation inhibitor. PLoS One. 5(6):e11101.
Magno A., Caflisch A., Pellarin R..  2010.  Crowding effects on amyloid aggregation kinetics. The Journal of Physical Chemistry Letters. 1(20):3027-3032.
Sonda S., Morf L., Bottova I., Baetschmann H., Rehrauer H., Caflisch A., Hakimi M.-A., Hehl A.B.  2010.  Epigenetic mechanisms regulate stage differentiation in the minimized protozoan Giardia lamblia. Molecular Microbiology. 76(1):48-67.
Qi B., Muff S., Caflisch A., Dinner A.R.  2010.  Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein. The Journal of Physical Chemistry B. 114(20):6979-6989.

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