Biblio

Found 274 results
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.
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.
Marchand F., Caflisch A..  2010.  Fast analytical continuum treatments of solvation. Modeling Solvent Environments: Applications to Simulations of Biomolecules. :209-232.
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.
Exner V., Alexandre C., Rosenfeldt G., Alfarano P., Nater M., Caflisch A., Gruissem W., Batschauer A., Hennig L..  2010.  A gain-of-function mutation of Arabidopsis cryptochrome1 promotes flowering. Plant Physiology. 154(4):1633-1645.
Zhou T., Caflisch A..  2010.  High-throughput virtual screening using quantum mechanical probes: Discovery of selective kinase inhibitors. ChemMedChem. 5(7):1007-1014.
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.
Vitalis A., Caflisch A..  2010.  Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-β peptide in aqueous solution and its implications for Aβ aggregation. Journal of Molecular Biology. 403(1):148-165.
Friedman R., Caflisch A..  2010.  On the orientation of the catalytic dyad in aspartic proteases. Proteins. 78(6):1575-1582.
Messner S., Altmeyer M., Zhao H., Pozivil A., Roschitzki B., Gehrig P., Rutishauser D., Huang D., Caflisch A., Hottiger M.O.  2010.  PARP1 ADP-ribosylates lysine residues of the core histone tails. Nucleic Acids Research. 38(19):6350-6362.
Zhou T., Huang D., Caflisch A..  2010.  Quantum mechanical methods for drug design. Current Topics in Medicinal Chemistry. 10(1):33-45.

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