Biblio

Found 274 results
2003
Levy Y., Caflisch A..  2003.  Flexibility of monomeric and dimeric HIV-1 protease. The Journal of Physical Chemistry B. 107(13):3068-3079.
Caflisch A..  2003.  Folding for binding or binding for folding? Trends in Biotechnology. 21(10):423-425.
Rao F., Caflisch A..  2003.  Replica exchange molecular dynamics simulations of reversible folding. The Journal of Chemical Physics. 119(7):4035-4042.
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.
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
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.
Majeux N., Scarsi M., Tenette-Souaille C., Caflisch A..  2002.  Hydrophobicity maps and docking of molecular fragments with solvation. Virtual Screening: An Alternative or Complement to High Throughput Screening? . 20:145-169.
Gsponer J., Caflisch A..  2002.  Molecular dynamics simulations of protein folding from the transition state. Proceedings of the National Academy of Sciences of the United States of America. 99(10):6719-6724.
Taufer M., Perathoner E., Cavalli A., Caflisch A., Stricker T..  2002.  Performance characterization of a molecular dynamics code on PC clusters: Is there any easy parallelism in CHARMM? Parallel and Distributed Processing Symposium, Proceedings International (IPDPS 2002).
Cavalli A., Ferrara P., Caflisch A..  2002.  Weak temperature dependence of the free energy surface and folding pathways of structured peptides.. Proteins: Structure, Function, and Bioinformatics. 47(3):305-314.
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.
Budin N., Ahmed S., Majeux N., Caflisch A..  2001.  An evolutionary approach for structure-based design of natural and non-natural peptidic ligands. Combinatorial Chemistry & High Throughput Screening. 4(8):661-673.
Tenette-Souaille C., Budin N., Majeux N., Caflisch A..  2001.  Fast continuum electrostatics methods for structure-based ligand docking. Combinatorial Library Design and Evaluation. :197-231.
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.
Paci E., Caflisch A., Plückthun A., Karplus M..  2001.  Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study. Journal of Molecular Biology. 314(3):589-605.
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.
Ferrara P., Caflisch A..  2001.  Native topology or specific interactions: What is more important for protein folding? Journal of Molecular Biology. 306(4):837-850.
Gsponer J., Caflisch A..  2001.  Role of native topology investigated by multiple unfolding simulations of four SH3 domains. Journal of Molecular Biology. 309(1):285-298.
Budin N., Majeux N., Tenette-Souaille C., Caflisch A..  2001.  Structure-based ligand design by a build-up approach and genetic algorithm search in conformational space. Journal of Computational Chemistry. 22(16):1956–1970.
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.
Caflisch A., Schramm H.J, Karplus M..  2000.  Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach. Journal of Computer-Aided Molecular Design. 14(2):161-179.
Ferrara P., Caflisch A..  2000.  Folding simulations of a three-stranded antiparallel β-sheet peptide. Proceedings of the National Academy of Sciences of the United States of America. 97(20):10780-10785.
Hiltpold A., Ferrara P., Gsponer J., Caflisch A..  2000.  Free energy surface of the helical peptide Y(MEARA)6. The Journal of Physical Chemistry B. 104(43):10080-10086.

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