Biblio

Found 17 results
Filters: Author is Caflisch, A. and Keyword is Models, Chemical  [Clear All Filters]
2009
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.
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.
2008
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.
Haberthür U., Caflisch A..  2008.  FACTS: Fast analytical continuum treatment of solvation. Journal of Computational Chemistry. 29(5):701-715.
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.
Seeber M., Cecchini M., Rao F., Settanni G., Caflisch A..  2007.  Wordom: A program for efficient analysis of molecular dynamics simulations. Bioinformatics. 23(19):2625-2627.
2006
Caflisch A..  2006.  Computational models for the prediction of polypeptide aggregation propensity. Current Opinion in Chemical Biology. 10(5):437-444.
Seeber M., Fanelli F., Paci E., Caflisch A..  2006.  Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane. Biophysical Journal. 91(9):3276-3284.
2005
Tartaglia G.G, Cavalli A., Pellarin R., Caflisch A..  2005.  Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences. Protein Science. 14(10):2723-2734.
2004
Levy Y., Caflisch A., Onuchic J.N, Wolynes P.G.  2004.  The folding and dimerization of HIV-1 protease: Evidence for a stable monomer from simulations. Journal of Molecular Biology. 340(1):67-79.
Settanni G., Gsponer J., Caflisch A..  2004.  Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations. Biophysical Journal. 86(3):1691-1701.
Caflisch A..  2004.  Protein folding: Simple models for a complex process. Structure. 12(10):1750-1752.
Cecchini M., Rao F., Seeber M., Caflisch A..  2004.  Replica exchange molecular dynamics simulations of amyloid peptide aggregation. Journal of Chemical Physics. 121(21):10748-10756.
2003
Cavalli A., Haberthür U., Paci E., Caflisch A..  2003.  Fast protein folding on downhill energy landscape. Protein Science. 12(8):1801-1803.
Werner P., Caflisch A..  2003.  A sphere-based model for the electrostatics of globular proteins. Journal of the American Chemical Society. 125(15):4600-4608.
2002
Ferrara P., Apostolakis J., Caflisch A..  2002.  Evaluation of a fast implicit solvent model for molecular dynamics simulations.. Proteins: Structure, Function, and Bioinformatics. 46(1):24-33.
2001
Majeux N., Scarsi M., Caflisch A..  2001.  Efficient electrostatic solvation model for protein-fragment docking. Proteins: Structure, Function, and Bioinformatics. 42(2):256-268.