Biblio

Found 53 results
Filters: Author is Caflisch, A. and Keyword is Protein Conformation  [Clear All Filters]
2007
Schroeder V., Vuissoz J.-M., Caflisch A., Kohler H.P.  2007.  Factor XIII activation peptide is released into plasma upon cleavage by thrombin and shows a different structure compared to its bound form. Thrombosis and Haemostasis. 97(6):890-898.
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.  Network and graph analyses of folding free energy surfaces. Current Opinion in Structural Biology. 16(1):71-78.
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
Gorfe A.A, Caflisch A..  2005.  Functional plasticity in the substrate binding site of beta-secretase. Structure. 13(10):1487-1498.
Tartaglia G.G, Pellarin R., Cavalli A., Caflisch A..  2005.  Organism complexity anti-correlates with proteomic beta-aggregation propensity. Protein Science. 14(10):2735-2740.
Böckmann R.A, Caflisch A..  2005.  Spontaneous formation of detergent micelles around the outer membrane protein OmpX. Biophysical Journal. 88(5):3191-3204.
2004
Cecchini M., Kolb P., Majeux N., Caflisch A..  2004.  Automated docking of highly flexible ligands by genetic algorithms: A critical assessment. Journal of Computational Chemistry. 25(3):412-422.
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.
Tartaglia G.G, Cavalli A., Pellarin R., Caflisch A..  2004.  The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates. Protein Science. 13(7):1939-1941.
Gorfe A.A, Caflisch A., Jelesarov I..  2004.  The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: A molecular dynamics analysis. Journal of Molecular Recognition. 17(2):120-131.
2003
Haberthür U., Majeux N., Werner P., Caflisch A..  2003.  Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution. Journal of Computational Chemistry. 24(15):1936-1949.
Gsponer J., Haberthür U., Caflisch A..  2003.  The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35. Proceedings of the National Academy of Sciences of the United States of America. 100(9):5154-5159.
2002
Gorfe A.A, Ferrara P., Caflisch A., Marti D.N, Bosshard H.R, Jelesarov I..  2002.  Calculation of protein ionization equilibria with conformational sampling: pKa of a model leucine zipper, GCN4 and barnase. Proteins: Structure, Function, and Bioinformatics. 46(1):41-60.
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
Gsponer J., Ferrara P., Caflisch A..  2001.  Flexibility of the murine prion protein and its Asp178Asn mutant investigated by molecular dynamics simulations. Journal of Molecular Graphics and Modelling. 20(2):169-182.
Budin N., Majeux N., Caflisch A..  2001.  Fragment-based flexible ligand docking by evolutionary optimization. Biological Chemistry. 382(9):1365-1372.
Ahmed S., Majeux N., Caflisch A..  2001.  Hydrophobicity and functionality maps of farnesyltransferase. Journal of Molecular Graphics and Modelling. 19(3-4):307-317.
2000
Ferrara P., Apostolakis J., Caflisch A..  2000.  Computer simulations of protein folding by targeted molecular dynamics. Proteins: Structure, Function, and Bioinformatics. 39(3):252-260.
1999
Scarsi M., Majeux N., Caflisch A..  1999.  Hydrophobicity at the surface of proteins. Proteins: Structure, Function, and Bioinformatics. 37(4):565-755.
Galzitskaya O., Caflisch A..  1999.  Solution conformation of phakellistatin 8 investigated by molecular dynamics simulations.. Journal of Molecular Graphics and Modelling. 17(1):19-27.
1996
Caflisch A..  1996.  Computational combinatorial ligand design: application to human α-thrombin. Journal of Computer-Aided Molecular Design. 10(5):372-396.
1995
Caflisch A., Karplus M..  1995.  Acid and thermal denaturation of barnase investigated by molecular dynamics simulations.. Journal of Molecular Biology. 252(5):672-708.

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