Found 274 results
Schuetz P., Caflisch A..  2008.  Efficient modularity optimization by multistep greedy algorithm and vertex mover refinement. Physical Review E: Statistical, Nonlinear, and Soft Matter Physics. 77(4.2):046112.
Haberthür U., Caflisch A..  2008.  FACTS: Fast analytical continuum treatment of solvation. Journal of Computational Chemistry. 29(5):701-715.
Dey F., Caflisch A..  2008.  Fragment-based de novo ligand design by multiobjective evolutionary optimization. Journal of Chemical Information and Modeling. 48(3):679-690.
Muff S., Caflisch A..  2008.  Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein. Proteins: Structure, Function, and Bioinformatics. 70(4):1185-1195.
Schuetz P., Caflisch A..  2008.  Multistep greedy algorithm identifies community structure in real-world and computer-generated networks. Physical Review E: Statistical, Nonlinear, and Soft Matter Physics. 78(2.2):026112.
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.
Zhou T., Huang D., Caflisch A..  2008.  Is quantum mechanics necessary for predicting binding free energy? Journal of Medicinal Chemistry. 51(14):4280-4288.
Kolb P., Kipouros C.B, Huang D., Caflisch A..  2008.  Structure-based tailoring of compound libraries for high-throughput screening: Discovery of novel EphB4 kinase inhibitors. Proteins: Structure, Function, and Bioinformatics. 73(1):11-18.
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.
Tartaglia G.G, Caflisch A..  2007.  Computational analysis of the S. cerevisiae proteome reveals the function and cellular localization of the least and most amyloidogenic proteins. Proteins: Structure, Function, and Bioinformatics. 68(1):273-278.
Rao F., Settanni G., Caflisch A..  2007.  Estimation of folding probabilities and Phi values from molecular dynamics simulations of reversible peptide folding. Protein Folding Protocols. :225-249.
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.
Pellarin R., Guarnera E., Caflisch A..  2007.  Pathways and intermediates of amyloid fibril formation. Journal of Molecular Biology. 374(4):917-924.
Friedman R., Caflisch A..  2007.  The protonation state of the catalytic aspartates in plasmepsin II. FEBS Letters. 581(21):4120-4124.
Gorfe A.A, Caflisch A..  2007.  Ser170 controls the conformational multiplicity of the loop 166-175 in prion proteins: Implication for conversion and species barrier. FASEB J. 21(12):3279-3287.
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.
Kolb P., Caflisch A..  2006.  Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking. Journal of Medicinal Chemistry. 49(25):7384-7392.
Caflisch A..  2006.  Computational models for the prediction of polypeptide aggregation propensity. Current Opinion in Chemical Biology. 10(5):437-444.
Huang D., Lüthi U., Kolb P., Cecchini M., Barberis A., Caflisch A..  2006.  In silico discovery of beta-secretase inhibitors. Journal of the American Chemical Society. 128(16):5436-5443.
Pellarin R., Caflisch A..  2006.  Interpreting the aggregation kinetics of amyloid peptides. Journal of Molecular Biology. 360(4):882-892.
Cecchini M., Curcio R., Pappalardo M., Melki R., Caflisch A..  2006.  A molecular dynamics approach to the structural characterization of amyloid aggregation. Journal of Molecular Biology. 357(4):1306-1321.
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.
Interlandi G., Settanni G., Caflisch A..  2006.  Unfolding transition state and intermediates of the tumor suppressor p16INK4a investigated by molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics. 64(1):178-192.