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Department of Biochemistry

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Publications Caflisch Group since 2010 (in alphabetical order)

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2015
Herrmann, US., Schütz, AK., Shirani, H., Huang, D., Saban, D., Nuvolone, M., Li, B., Ballmer, B., Åslund, AK., Mason, JJ., Rushing, E., Budka, H., Nyström, S., Hammarström, P., Böckmann, A., Caflisch, A., Meier, BH., Nilsson, KP., Hornemann, S. & Aguzzi, A. Structure-based drug design identifies polythiophenes as antiprion compounds. Sci Transl Med 7, 299ra123 (2015). PMID: 26246168.

Xu, M., Unzue, A., Dong, J., Spiliotopoulos, D., Nevado, C. & Caflisch, A. Discovery of CREBBP Bromodomain Inhibitors by High-Throughput Docking and Hit Optimization Guided by Molecular Dynamics. J. Med. Chem. [Epub ahead of print] (2015). PMID: 26125948.

Unzue, A., Xu, M., Dong, J., Wiedmer, L., Spiliotopoulos, D., Caflisch, A. & Nevado, C. Fragment-Based Design of Selective Nanomolar Ligands of the CREBBP Bromodomain. J. Med. Chem. [Epub ahead of print] (2015). PMID: 26043365.

Marchand, JR. & Caflisch, A. Binding Mode of Acetylated Histones to Bromodomains: Variations on a Common Motif. ChemMedChem 10, 1327-33 (2015). PMID: 26033856.

Blöchliger, N., Xu, M. & Caflisch, A. Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges. Biophys. J. 108, 2362-70 (2015). PMID: 25954893.

Zhao, H. & Caflisch, A. Current kinase inhibitors cover a tiny fraction of fragment space. Bioorg. Med. Chem. Lett. 25, 2372-6 (2015). PMID: 25911301.

Ewald, C., Christen, MT., Watson, RP., Mihajlovic, M., Zhou, T., Honegger, A., Plückthun, A., Caflisch, A. & Zerbe, O. A combined NMR and computational approach to investigate peptide binding to a designed Armadillo repeat protein. J. Mol. Biol. 427, 1916-33 (2015). PMID: 25816772.

Huang, D. & Caflisch, A. Evolutionary conserved Tyr169 stabilizes the β2-α2 loop of the prion protein. J. Am. Chem. Soc. 137, 2948-57 (2015). PMID: 25671636.

Dong, J., Zhao, H., Zhou, T., Spiliotopoulos, D., Rajendran, C., Li, XD., Huang, D. & Caflisch, A. Structural Analysis of the Binding of Type I, I1/2, and II Inhibitors to Eph Tyrosine Kinases. ACS Med Chem Lett 6, 79-83 (2015). PMID: 25589935.

Müller, CS., Knehans, T., Davydov, DR., Bounds, PL., von Mandach, U., Halpert, JR., Caflisch, A. & Koppenol, WH. Concurrent cooperativity and substrate inhibition in the epoxidation of carbamazepine by cytochrome P450 3A4 active site mutants inspired by molecular dynamics simulations. Biochemistry 54, 711-21 (2015). PMID: 25545162.

Bacci, M., Vitalis, A. & Caflisch, A. A molecular simulation protocol to avoid sampling redundancy and discover new states. Biochim. Biophys. Acta 1850, 889-902 (2015). PMID: 25193737

Holehouse, AS., Garai, K., Lyle, N., Vitalis, A. & Pappu, RV. Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation. J. Am. Chem. Soc. 137, 2984-95 (2015). PMID: 25664638.

2014
Bacci, M., Vitalis, A. & Caflisch, A. A molecular simulation protocol to avoid sampling redundancy and discover new states. Biochim. Biophys. Acta [Epub ahead of print] (2014). PMID: 25193737.

Blöchliger, N., Vitalis, A. & Caflisch, A. High-resolution visualisation of the States and pathways sampled in molecular dynamics simulations. Sci Rep 4, 6264 (2014). PMID: 25179558.

Friedman, R. & Caflisch, A. Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: A simulation study. Proteins 82, 399-404 (2014). PMID: 24038616.

Fu, B., Sahakyan, AB., Camilloni, C., Tartaglia, GG., Paci, E., Caflisch, A., Vendruscolo, M. & Cavalli, A. ALMOST: An all atom molecular simulation toolkit for protein structure determination. J Comput Chem 35, 1101-5 (2014). PMID: 24676684.

Huang, D., Rossini, E., Steiner, S. & Caflisch, A. Structured water molecules in the binding site of bromodomains can be displaced by cosolvent. ChemMedChem 9, 573-9 (2014). PMID: 23804246.

Novinec, M., Korenč, M., Caflisch, A., Ranganathan, R., Lenarčič, B. & Baici, A. A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods. Nat Commun 5, 3287 (2014). PMID: 24518821.

Pevzner, Y., Frugier, E., Schalk, V., Caflisch, A. & Woodcock, HL. Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design. J Chem Inf Model 54, 2612-20 (2014). PMID: 25151852.

Pochorovski, I., Knehans, T., Nettels, D., Müller, AM., Schweizer, WB., Caflisch, A., Schuler, B. & Diederich, F. Experimental and Computational Study of BODIPY Dye-Labeled Cavitand Dynamics. J. Am. Chem. Soc. 136, 2441-9 (2014). PMID: 24490940.

Unzue, A., Dong, J., Lafleur, K., Zhao, H., Frugier, E., Caflisch, A. & Nevado, C. Pyrrolo[3,2-b]quinoxaline Derivatives as Types I1/2 and II Eph Tyrosine Kinase Inhibitors: Structure-Based Design, Synthesis, and in Vivo Validation. J. Med. Chem. 57, 6834-44 (2014). PMID: 25076195.

Vitalis, A. & Caflisch, A. Equilibrium sampling approach to the interpretation of electron density maps. Structure 22, 156-67 (2014). PMID: 24316403.

Watson, RP., Christen, MT., Ewald, C., Bumbak, F., Reichen, C., Mihajlovic, M., Schmidt, E., Güntert, P., Caflisch, A., Plückthun, A. & Zerbe, O. Spontaneous Self-Assembly of Engineered Armadillo Repeat Protein Fragments into a Folded Structure. Structure 22, 985-95 (2014). PMID: 24931467.

Zhao, H., Gartenmann, L., Dong, J., Spiliotopoulos, D. & Caflisch, A. Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking. Bioorg. Med. Chem. Lett. 24, 2493-6 (2014). PMID: 24767840.

Zhao, H. & Caflisch, A. Molecular dynamics in drug design. Eur J Med Chem [Epub ahead of print] (2014). PMID: 25108504.

Zhao, H. & Caflisch, A. Discovery of dual ZAP70 and Syk kinases inhibitors by docking into a rare C-helix-out conformation of Syk. Bioorg. Med. Chem. Lett. 24, 1523-7 (2014). PMID: 24569110.

Zhou, T., Georgeon, S., Moser, R., Moore, DJ., Caflisch, A. & Hantschel, O. Specificity and mechanism-of-action of the JAK2 tyrosine kinase inhibitors ruxolitinib and SAR302503 (TG101348). Leukemia 28, 471-2 (2014). PMID: 24496285.

2013
Attanasio, F., Convertino, M., Magno, A., Caflisch, A., Corazza, A., Haridas, H., Esposito, G., Cataldo, S., Pignataro, B., Milardi, D. & Rizzarelli, E. Carnosine inhibits ABeta(42) aggregation by perturbing the H-bond network in and around the central hydrophobic cluster. Chembiochem 14, 583-592 (2013).

Buchli, B., Waldauer, SA., Walser, R., Donten, ML., Pfister, R., Blöchliger, N., Steiner, S., Caflisch, A., Zerbe, O. & Hamm, P. Kinetic response of a photoperturbed allosteric protein. PNAS 110, 11725-11730 (2013).

Kalgin, IV., Caflisch, A., Chekmarev,SF. & Karplus, M. New insights into the folding of a beta sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow. J Phys Chem B. 117, 6092-6105 (2013). 

Lafleur, K., Dong, J., Huang, D., Caflisch, A. & Nevado, C. Optimization of inhibitors of the tyrosine kinase EphB4.2. cellular potency improvement and binding mode validation by X-ray crystallography.  J Med Chem. 56, 84-96 (2013).

Rosenthal, F., Feijs, KL., Frugier, E., Bonalli, M., Forst, AH., Imhof, R., Winkler, HC., Fischer, D., Caflisch, A., Hassa, PO., Lüscher, B. & Hottiger, MO. Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases. Nat Struct. Mol. Biol. 20, 502-507 (2013).

Scherzer-Attali, R., Convertino, M., Pellarin, R., Caflisch, A., Gazit, E. & Segal, D. Methylations of tryptophan modified naphtoquinone affect its inhibitory potential towards Abeta aggregation. J Phys Chem B. 117, 1780-1789 (2013).

Steiner, S, Magno, A., Huang, D. & Caflisch, A. Does bromodomain flexibility influence histone recognition? FEBS Lett. 587, 2158-2163 (2013).

Zhao, H. & Caflisch, A. Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics. Bioorg. Med. Chem. Lett. 23, 5721-6 (2013).

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

Adler-Abramovich, L., Vaks, L., Carny, O., Trudler, D., Magno, A., Caflisch, A., Frenkel, D. & Gazit, E. Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylkentonuria. Nat Chem Biol 8, 701-706 (2012).

Caflisch, A. & Hamm, P. Complexity in protein folding: simulation meets experiment. Curr Phys Chem. 2, 4-11 (2012).

Huang, D. & Caflisch, A. How does Darunavir prevent HIV-1 protease dimerization? J Chem Theory Comput. 8, 1786-1794 (2012).

Magno, A,, Pellarin, R. & Caflisch, A. Mechanisms and kinetics of amyloid aggregation investigated by a phenomenological coarse-grained model. In: Computational Modelling of Biological Systems, eds. N. Dokholyan, Springer 2012, pp. 191 ff.

Radhakrishnan, A., Vitalis, A., Mao, AH., Steffen, AT. & Pappu, RV. Improved atomistic Monte Carlo simulations demonstrate that poly-l-proline adopts heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks. J Phys Chem B. 116, 6862-6871 (2012).

Rennebaum, S. & Caflisch, A. Inhibition of interdomain motion in G-actin by the natural product latrunculin: a molecular dynamics study. Proteins. 80, 1998-2008 (2012). 

Scalco, R. & Caflisch, A. Ultrametricity in protein folding dynamics. J Chem Theory Comput. (2012).

Steiner, S. & Caflisch, A. Peptide binding to the PDZ3 domain by conformational selection. Proteins. 80, 2562-2572 (2012).

Vitalis, A. & Caflisch, A. Efficient construction of mesostate networks from molecular dynamics trajectories.  J Chem Theory Comput. 8, 1108-1120 (2012).

Vitalis, A. & Caflisch, A. 50 years of Lifson-Roig models: applications to molecular simulation data. J Chem Theory Comput. 8, 363-373 (2012).

Waldauer,SA., Hassan, S., Paoli, B., Donaldson, PM, Pfister, R., Hamm, P., Caflisch, A. & Pellarin, R. Photocontrol of reversible amyloid formation with a minimal-design peptide. J. Phys. Chem. B. 116, 8961-8973 (2012).

Zhao, H., Huang, D. & Caflisch, A. Discovery of tyrosine kinase inhibitors by docking into an inactive kinase conformation generated by molecular dynamics. ChemMedChem. 2012  Sep 13.  [Epub ahead of print]

2011
Convertino, M., Vitalis, A. & Caflisch, A. Disordered binding of small molecules to A beta12-28. J Biol Chem. 414, 303-312 (2011).

Friedman, R. & Caflisch, A. Surfactant effects of amyloid aggregation kinetics. J Mol. Biol. 414, 303-312 (2011).

Frydman-Marom, A., Convertino. M., Pellarin, R., Lampel, A., Shaltiel-Karyo, R., Segal, D., Caflisch, A., Shalev, DE. & Gazit, E. Structural basis for inhibiting beta amyloid oligomerization by a non-coded beta-breaker-substituted endomorphin analogue. ACS Chem Biol. 6, 1265-1276 (2011).

Ganesan, R., Jelakovic, S., Mittl, PR., Caflisch, A. & Grütter, MG. In silico identification and crystal structure validation of procaspase-3 inhibitors without a P1 aspartic acid moiety. Acta Crystallogr SectF Struct Biol Cryst Commun. 67(Pt8), 842-850 (2011).

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

Huang, D. & Caflisch, A. The free energy landscape of small molecule unbinding. PLoS Comput. Biol. 7 (2): e1002002 (2011).

Mishra, S. & Caflisch, A .Dynamics in the active site of beta secretase: a network analysis of atomistic simulations. Biochemistry 50, 9328-9339 (2011).

Scalco, R. & Caflisch, A. Equilibrium distribution from distributed computing (simulations of protein folding). J. Phys. Chem B. 115, 6358-6365 (2011).

Seeber, M., Felline, A., Raimondi, F., Muff, S., Friedmann, R., Rao, F., Caflisch, A. & Fanelli, F. Wordom: a user-friendly program for the analysis of molecular structures, trajectories and free energy surfaces. J Comput Chem. 32, 1183-1194 (2011).

Zhao, H. & Huang, D. Hydrogen bond penalty upon ligand binding. PLoS One 6(6): e19923 (2011).

Zheng, W., Qi, B., Rohrdanz, MA., Caflisch, A., Dinner, AR. & Clementi, C. Delineation of folding pathways of a beta-sheet mini-protein. J Phys Chem B. 115, 13065-13074 (2011).

2010
Backus, EH., Bloem, R., Donaldson, PM., Ihalainen, JA., Pfister, R., Paoli, B., Caflisch, A. & Hamm, P. 2D-IR study of a photoswitchable isoptope-labeled alpha-helix. J. Phys. Chem. B. 114, 3735-40 (2010).

Exner,V., Alexandre, C., Rosenfeldt, G., Alfarano, P., Nater, M., Caflisch, A., Gruissem, W., Batschauer, A. & Hennig, L. A gain-of-function mutation of arabidopsis CRYPTOCHROME1 promotes flowering. Plant Physiol. 154, 1633-1645 (2010).

Friedmannn, R. & Caflisch, A. On the orientation of the catalytic dyad in aspartic proteases. Proteins 78, 1575-1582 (2010).  

Friedmannn, R. , Pellarin , R. & Caflisch, A. Soluble protofibrils as metastable intermediates in simulations of amyloid fibril degradation induced by lipid vesicles. J. Physical Chem. Letters 1, 471-474 (2010).

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

Huang, D. & Caflisch, A. Library screening by fragment-based docking. J. Mol. Recognit. 23, 183-193 (2010).

Kaiser-Bunbury, CN., Muff, S., Memmott, J., Müller, CB. & Caflisch, A. The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour. Ecol Lett. 13, 442-452  (2010).

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

Paoli,B., Pellarin, R. & Caflisch, A. Slow folding of cross-linked alpha-helical peptides due to steric hindrance. J Phys Chem B. 114, 2023-2027 (2010).

Pellarin, R., Schütz, P., Guarnera, E. & Caflisch, A. Amyloid fibril polymorphism is under kinetic control. J Am Chem Soc. 132, 14960-14970 (2010). 

Qi, B., Muff, S., Caflisch, A. & Dinner, AR. Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein. J Phys Chem B. 114, 6979-6989 (2010).

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

Schütz, P., Wuttke, R., Schuler, B. & Caflisch, A. Free energy surfaces from single-distance information. J. Phys. Chem. B. 114, 15227-15235 (2010).  

Sonda S., Morf, L., Bottova, I., Baetschmann, H., Rehrauer, H., Caflisch, A., Hakimi, MA. & Hehl, AB. Epigenetic mechanisms regulate stage differentiation in the minimized protozoan Giardia lamblia. Mol Microbiol. 76, 48-67 (2010).

Vitalis, A. & Caflisch, A. Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-beta peptide in aqueous solution and its implications for abeta aggregation. J Mol Biol. 403, 148-165  (2010).

Zhou, T., Lafleur, K. & Caflisch,A. Complementing ultrafast shape recognition with an optical isomerism descriptor. J Mol Graph Model. 29, 443-449 (2010).

Zhou, T. , Huang, D. & Caflisch, A. Quantum mechanical methods for drug design. Curr. Top. Med. Chem 10, 33-45 (2010).

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

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