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Esposito, C; Wiedmer, L; Caflisch, A (2018). In Silico Identification of JMJD3 Demethylase Inhibitors. Journal of Chemical Information and Modeling, 58(10):2151-2163.

Unzue, A; Cribiú, R; Hoffman, M M; Knehans, T; Lafleur, K; Caflisch, A; Nevado, C (2018). Iriomoteolides: novel chemical tools to study actin dynamics. Chemical Science, 9(15):3793-3802.

Zhou, T; Georgeon, S; Moser, R; Moore, D J; Caflisch, A; Hantschel, O (2014). Specificity and mechanism-of-action of the JAK2 tyrosine kinase inhibitors ruxolitinib and SAR302503 (TG101348). Leukemia, 28(2):404-407.

Caflisch, A; Hamm, P (2012). Complexity in Protein Folding: Simulation Meets Experiment. Current Physical Chemistry, 2:4-11.

Alfarano, P; Varadamsetty, G; Ewald, C; Parmeggiani, F; Pellarin, R; Zerbe, O; Plückthun, A; Caflisch, A (2012). Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy. Protein Science, 21(9):1298-1314.

Zheng, W; Qi, B; Rohrdanz, M A; Caflisch, A; Dinner, A R; Clementi, C (2011). Delineation of folding pathways of a β-sheet miniprotein. Journal of Physical Chemistry. B, 115(44):13065-13074.

Convertino, M; Vitalis, A; Caflisch, A (2011). Disordered binding of small molecules to aβ(12-28). Journal of Biological Chemistry, 286(48):41578-41588.

Mishra, S; Caflisch, A (2011). Dynamics in the active site of β-Secretase: a network analysis of atomistic simulations. Biochemistry, 50(43):9328-9339.

Scalco, R; Caflisch, A (2011). Equilibrium distribution from distributed computing (simulations of protein folding). Journal of Physical Chemistry. B, 115(19):6358-6365.

Ganesan, R; Jelakovic, S; Mittl, P R E; Caflisch, A; Grütter, M G (2011). In silico identification and crystal structure validation of caspase-3 inhibitors without a P1 aspartic acid moiety. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications, 67(Pt 8):842-850.

Huang, D; Caflisch, A (2011). Small molecule binding to proteins: affinity and binding/unbinding dynamics from atomistic simulations. ChemMedChem, 6(9):1578-1580.

Frydman-Marom, A; Convertino, M; Pellarin, R; Lampel, A; Shaltiel-Karyo, R; Segal, D; Caflisch, A; Shalev, D E; Gazit, E (2011). Structural basis for inhibiting β-amyloid oligomerization by a non-coded β-breaker-substituted endomorphin analogue. ACS Chemical Biology, 6(11):1265-1276.

Friedman, R; Caflisch, A (2011). Surfactant effects on amyloid aggregation kinetics. Journal of Molecular Biology, 414(2):303-312.

Huang, D; Caflisch, A (2011). The free energy landscape of small molecule unbinding. PLoS Computational Biology, 7(2):e1002002.

Seeber, M; Felline, A; Raimondi, F; Muff, S; Friedman, R; Rao, F; Caflisch, A; Fanelli, F (2011). Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. Journal of Computational Chemistry, 32(6):1183-1194.

Messner, S; Altmeyer, M; Zhao, H; Pozivil, A; Roschitzki, B; Gehrig, P; Rutishauser, D; Huang, D; Caflisch, A; Hottiger, M O (2010). PARP1 ADP-ribosylates lysine residues of the core histone tails. Nucleic Acids Research, 38(19):6350-6362.

Kaiser-Bunbury, C N; Muff, S; Memmott, J; Müller, C B; Caflisch, A (2010). The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour. Ecology Letters, 13(4):442-452.

Backus, E H G; Bloem, R; Donaldson, P M; Ihalainen, J A; Pfister, R; Paoli, B; Caflisch, A; Hamm, P (2010). 2D-IR Study of a Photoswitchable Isotope-Labeled α-Helix. Journal of Physical Chemistry. B, 114(10):3735-3740.

Huang, D; Caflisch, A (2010). Library screening by fragment-based docking. Journal of Molecular Recognition, 23(2):183-193.

Sonda, S; Morf, L; Bottova, I; Baetschmann, H; Rehrauer, H; Caflisch, A; Hakimi, M-A; Hehl, A B (2010). Epigenetic mechanisms regulate stage differentiation in the minimized protozoan Giardia lamblia. Molecular Microbiology, 76(1):48-67.

Exner, V; Alexandre, C; Rosenfeldt, G; Alfarano, P; Nater, M; Caflisch, A; Gruissem, W; Batschauer, A; Hennig, L (2010). A gain-of-function mutation of Arabidopsis cryptochrome1 promotes flowering. Plant Physiology, 154(4):1633-1645.

Pellarin, R; Schuetz, P; Guarnera, E; Caflisch, A (2010). Amyloid fibril polymorphism is under kinetic control. Journal of the American Chemical Society, 132(42):14960-14970.

Zhou, T; Lafleur, K; Caflisch, A (2010). Complementing ultrafast shape recognition with an optical isomerism descriptor. Journal of Molecular Graphics and Modelling, 29(3):443-449.

Scherzer-Attali, R; Pellarin, R; Convertino, M; Frydman-Marom, A; Egoz-Matia, N; Peled, S; Levy-Sakin, M; Shalev, D E; Caflisch, A; Gazit, E; Segal, D (2010). Complete phenotypic recovery of an Alzheimer's disease model by a quinone-tryptophan hybrid aggregation inhibitor. PLoS ONE, 5(6):e11101.

Magno, A; Caflisch, A; Pellarin, R (2010). Crowding effects on amyloid aggregation kinetics. Journal of Physical Chemistry Letters, (1):3027-3032.

Qi, B; Muff, S; Caflisch, A; Dinner, A R (2010). Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein. Journal of Physical Chemistry. B, 114(20):6979-6989.

Schuetz, P; Wuttke, R; Schuler, B; Caflisch, A (2010). Free energy surfaces from single-distance information. Journal of Physical Chemistry. B, 114(46):15227-15235.

Zhou, T; Caflisch, A (2010). High-throughput virtual screening using quantum mechanical probes: discovery of selective kinase inhibitors. ChemMedChem, 5(7):1007-1014.

Huang, D; Zhou, T; Lafleur, K; Nevado, C; Caflisch, A (2010). Kinase selectivity potential for inhibitors targeting the ATP binding site: A network analysis. Bioinformatics, 26(2):198-204.

Vitalis, A; Caflisch, A (2010). Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-β peptide in aqueous solution and its implications for Aβ aggregation. Journal of Molecular Biology, 403(1):148-165.

Friedman, R; Caflisch, A (2010). On the orientation of the catalytic dyad in aspartic proteases. Proteins, 78(6):1575-1582.

Zhou, T; Huang, D; Caflisch, A (2010). Quantum mechanical methods for drug design. Current Topics in Medicinal Chemistry, 10(1):33-45.

Paoli, B; Pellarin, R; Caflisch, A (2010). Slow folding of cross-linked alpha-helical peptides due to steric hindrance. Journal of Physical Chemistry. B, 114(5):2023-2027.

Friedman, R; Pellarin, R; Caflisch, A (2010). Soluble Protofibrils as Metastable Intermediates in Simulations of Amyloid Fibril Degradation Induced by Lipid Vesicles. Journal of Physical Chemistry Letters:471-474.

Friedman, R; Pellarin, R; Caflisch, A (2009). Amyloid aggregation on lipid bilayers and its impact on membrane permeability. Journal of Molecular Biology, 387(2):407-415.

Paoli, B; Seeber, M; Backus, E H; Ihalainen, J A; Hamm, P; Caflisch, A (2009). Bulky Side Chains and Non-native Salt Bridges Slow down the Folding of a Cross-Linked Helical Peptide: A Combined Molecular Dynamics and Time-Resolved Infrared Spectroscopy Study. Journal of Physical Chemistry. B, 113(13):4435-4442.

Muff, S; Caflisch, A (2009). Identification of the protein folding transition state from molecular dynamics trajectories. Journal of Chemical Physics, 130(12):125104.

Muff, S; Caflisch, A (2009). ETNA: Equilibrium Transitions Network and Arrhenius Equation for Extracting Folding Kinetics from REMD Simulations. Journal of Physical Chemistry. B, 113(10):3218-3226.

Ekonomiuk, D; Su, X-C; Ozawa, K; Bodenreider, C; Lim, S P; Yin, Z; Keller, T H; Beer, D; Patel, V; Otting, G; Caflisch, A; Huang, D (2009). Discovery of a non-peptidic inhibitor of west nile virus NS3 protease by high-throughput docking. PLoS Neglected Tropical Diseases, 3(1):e356.

Convertino, M; Pellarin, R; Catto, M; Carotti, A; Caflisch, A (2009). 9,10-Anthraquinone hinders beta-aggregation: how does a small molecule interfere with Abeta-peptide amyloid fibrillation? Protein Science, 18(4):792-800.

Bodenreider, C; Beer, D; Keller, T H; Sonntag, S; Wen, D; Yap, L; Yau, Y H; Shochat, S G; Huang, D; Zhou, T; Caflisch, A; Su, X C; Ozawa, K; Otting, G; Vasudevan, S G; Lescar, J; Lim, S P (2009). A fluorescence quenching assay to discriminate between specific and nonspecific inhibitors of dengue virus protease. Analytical Biochemistry, 395(2):195-204.

Ekonomiuk, D; Caflisch, A (2009). Activation of the West Nile virus NS3 protease: molecular dynamics evidence for a conformational selection mechanism. Protein Science, 18(5):1003-1011.

Brooks, B R; Brooks, C L; Mackerell, A D; Nilsson, L; Petrella, R J; Roux, B; Won, Y; Archontis, G; Bartels, C; Boresch, S; Caflisch, A; Caves, L; Cui, Q; Dinner, A R; Feig, M; Fischer, S; Gao, J; Hodoscek, M; Im, W; Kuczera, K; Lazaridis, T; Ma, J; Ovchinnikov, V; Paci, E; Pastor, R W; Post, C B; Pu, J Z; Schaefer, M; Tidor, B; Venable, R M; Woodcock, H L; Wu, X; Yang, W; York, D M; Karplus, M (2009). CHARMM: the biomolecular simulation program. Journal of Computational Chemistry, 30(10):1545-1614.

Zhou, T; Caflisch, A (2009). Data management system for distributed virtual screening. Journal of Chemical Information and Modeling, 49(1):145-152.

Friedman, R; Caflisch, A (2009). Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring. ChemMedChem, 4(8):1317-1326.

Ekonomiuk, D; Su, X C; Ozawa, K; Bodenreider, C; Lim, S P; Otting, G; Huang, D; Caflisch, A (2009). Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics. Journal of Medicinal Chemistry, 52(15):4860-4868.

Guarnera, E; Pellarin, R; Caflisch, A (2009). How does a simplified-sequence protein fold? Biophysical Journal, 97(6):1737-1746.

Su, X C; Ozawa, K; Yagi, H; Lim, S P; Wen, D; Ekonomiuk, D; Huang, D; Keller, T H; Sonntag, S; Caflisch, A; Vasudevan, S G; Otting, G (2009). NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease. FEBS Journal, 276(15):4244-4255.

Benedix, A; Becker, C M; de Groot, B L; Caflisch, A; Böckmann, R A (2009). Predicting free energy changes using structural ensembles. Nature Methods, 6(1):3-4.

Lafleur, K; Huang, D; Zhou, T; Caflisch, A; Nevado, C (2009). Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4). Journal of Medicinal Chemistry, 52(20):6433-6446.

Exner, V; Aichinger, E; Shu, H; Wildhaber, T; Alfarano, P; Caflisch, A; Gruissem, W; Köhler, C; Hennig, L (2009). The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development. PLoS ONE, 4(4):e5335.

Ihalainen, J A; Paoli, B; Muff, S; Backus, E H G; 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 (PNAS), 105(28):9588-9593.

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. Journal of Physical Chemistry. B, 112(29):8701-8714.

Schuetz, P; Caflisch, A (2008). Efficient modularity optimization by multistep greedy algorithm and vertex mover refinement. Physical Review E, 77(046112):046112-1-046112-7.

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, 73(1):11-8.

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.

Schenker, P; Alfarano, P; Kolb, P; Caflisch, A; Baici, A (2008). A double-headed cathepsin B inhibitor devoid of warhead. Protein Science : a Publication of the Protein Society, 17(12):2145-2155.

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.

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.

Zhou, T; Huang, D; Caflisch, A (2008). Is quantum mechanics necessary for predicting binding free energy? Journal of medicinal chemistry, 51(14):4280-4288.

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, 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, 78(026112):026112-1.

Friedman, R; Caflisch, A (2008). Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis. Proteins, 73(4):814-827.

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.

This list was generated on Wed Jun 26 16:14:15 2019 CEST.