Biblio

Found 304 results
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.
Parmeggiani F., Pellarin R., Larsen A.P, Varadamsetty G., Stumpp M.T, Zerbe O., Caflisch A., Plückthun A..  2008.  Designed armadillo repeat proteins as general peptide-binding scaffolds: Consensus design and computational optimization of the hydrophobic core. Journal of Molecular Biology. 376(5):1282-1304.
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.
Schenker P., Alfarano P., Kolb P., Caflisch A., Baici A..  2008.  A double-headed cathepsin B inhibitor devoid of warhead. Protein Science. 17(12):2145-2155.
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.
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.
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.
2006
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.

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