Biblio

Found 43 results
Filters: Author is Caflisch, A. and Keyword is Thermodynamics  [Clear All Filters]
2014
Vitalis A., Caflisch A..  2014.  Equilibrium sampling approach to the interpretation of electron density maps. Structure. 22(1):156-167.
Unzue A., Dong J., Lafleur K., Zhao H., Frugier E., Caflisch A., Nevado C..  2014.  Pyrrolo[3,2-b]quinoxaline derivatives as types I1/2 and II Eph tyrosine kinase inhibitors: Structure-based design, synthesis, and in vivo validation. Journal of Medicinal Chemistry. 57(15):6834-6844.
2013
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.
2012
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.
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.
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.
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
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.
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.
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.
Paoli B., Pellarin R., Caflisch A..  2010.  Slow folding of cross-linked alpha-helical peptides due to steric hindrance. The Journal of Physical Chemistry B. 114(5):2023-2027.
2009
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.
Muff S., Caflisch A..  2009.  Identification of the protein folding transition state from molecular dynamics trajectories. Journal of Chemical Physics. 130(12):125104.
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.
2008
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.
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.
Haberthür U., Caflisch A..  2008.  FACTS: Fast analytical continuum treatment of solvation. Journal of Computational Chemistry. 29(5):701-715.
Krivov S.V, Muff S., Caflisch A., Karplus M..  2008.  One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: New insights into the folding process. The Journal of Physical Chemistry B. 112(29):8701-8714.
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
Gfeller D., De Los Rios P., Caflisch A., Rao F..  2007.  Complex network analysis of free-energy landscapes. Proceedings of the National Academy of Sciences of the United States of America. 104(6):1817-1822.

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