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Department of Biochemistry

Calendar of Events

Publications Caflisch Group since 2010 (in alphabetical order)

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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

Blöchliger, N., Caflisch, A. & Vitalis, A. Weighted Distance Functions Improve Analysis of High-Dimensional Data: Application to Molecular Dynamics Simulations. J Chem Theory Comput 11, 5481-92 (2015). PMID: 26574336.

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.

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.

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.

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.

Huang, D. & Caflisch, A. The roles of the conserved tyrosine in the β2-α2 loop of the prion protein. Prion 9, 412-9 (2015). PMID: 26689486.

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.

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.

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

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.

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.

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.

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

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.

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).

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]

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).

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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