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Department of Biochemistry

Publications Caflisch Group 2004-2009 (in alphabetical order)

Benedix, A., Becker, CM., de Groot, BL., Caflisch, A. & Böckmann, R. Predicting free energy changes using structural ensembles. Nat. Methods 6, 3-4 (2009).

Bodenreider C, Beer D, Keller TH, Sonntag S, Wen D, Yap L, Yau YH, Shochat SG, Huang D, Zhou T, Caflisch A, Su XC, Ozawa K, Otting G, Vasudevan SG, Lescar J, Lim SP. A fluorescence quenching assay to discriminate between specific and non-specific inhibitors of Dengue virus. Anal Biochem. 395, 195-204 (2009). 

Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M. CHARMM: the biomolecular simulation program. J. Comput. Chem. 30, 1545-1614 (2009).

Convertino, M., Pellarin, R., Catto, M., Carotti, A. & Caflisch, A. 9,10-Anthraquinone hinders beta-aggregation: How does a small molecule interfere with Abeta-peptide amyloid fibrilles? Protein Sci. 18, 792-800 (2009).

Ekonomiuk, D. & Caflisch, A. Activation of the West Nile virus NS3 protease: molecular dynamics evidence for a conformational selection mechanism. Protein Sci. 18, 1003-11 (2009).

Ekonomiuk, D., Su, XC., Ozawa, K., Bodenreider, C., Lim, SP., Yin Z., Keller TH., Beer D., Patel V., Otting G., Caflisch A. & Huang D. Discovery of a non-peptidic inhibitor of west nile virus NS3 protease by high-throughput docking. PLoS Negl. Trp. Dis. 3(1): e356 (2009).

Ekonomiuk, D., Su, XC., Ozawa, K., Bodenreider, C., Lim, SP., Huang, D. & Caflisch A. Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics.  J Med Chem. 52, 4860-4868 (2009).

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

Friedmann, R. & Caflisch, A. Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring. Chem. Med. Chem. 4, 1317-1326 (2009).  

Friedmann, R., Pellarin, R. & Caflisch, A. Amyloid aggregation on lipid bilayers and its impact on membrane permeability. J. Mol. Biol. 387, 407-415 (2009).
Guarnera, E., Pellarin, R. & Caflisch, A. How does a simplified-sequence protein fold? Biophys. J. 97, 1737-1746 (2009). 

Huang, D. & Caflisch, A. Library screening by fragment-based docking. J Mol Recognit. 2009 Aug 28. [Epub ahead of print].

Interlandi, G. Backbone conformations and side chain flexibility of two somatostatin mimics investigated by molecular dynamics stimulation. Proteins 75, 659-670 (2009). 

Lafleur, K., Huang, D., Zhou, T., Caflisch, A. & Nevado, C. Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4). J Med Chem. 52, 6433-6446 (2009).

Muff, S. & Caflisch, A. ETNA: Equilibrium transitions network and Arrhenius equation for extracting folding kinetics from REMD simulations. J Phys Chem B. 113, 3218-3226 (2009).

Muff, S. & Caflisch, A. Identification of the protein folding transition state from molecular dynamics trajectories. J. Chem Phys. 130, 125104 (2009).

Paoli, B., Seeber, M., Backus, EH., Ihalainen, JA., Hamm, P. & Caflisch, A. 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. J Phys Chem B113, 4435-4442 (2009).

Su, XC, Ozawa, K, Yagi, H, Lim, SP, Wen, D, Ekonomiuk, D, Huang, D, Keller, TH, Sonntag, S, Caflisch, A, Vasudevan, SG & Otting G. NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease. FEBS J.  276, 4244-4255 (2009).

Zhou, T. & Caflisch, A. Data management system for distributed virtual screening. J. Chem. Inf. Model. 49, 145-152 (2009).

Dey, F. & Caflisch, A. Fragment-based de novo ligand design by multiobjective evolutionary optimization. J. Chem. Inf. Model. 48, 679-690 (2008).

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

Haberthür, U. & Caflisch , A. FACTS: Fast analytical continuum treatment of solvation. J. Computat. Chem29, 701-715 (2008). 

Ihalainen, JA., Paoli, B., Muff, S., Backus, EH., Bredenbeck, J., Woolley, GA., Caflisch, A. & Hamm, P. Alpha-Helix folding in the presence of structural constraints. PNAS USA 195, 9588-9593 (2008).

Interlandi, G., Wetzel, S.K., Settani, G. , Plückthun, A. & Caflisch, A. Characterization and further stabilization of designed ankyrin repeat proteins by combining molecular dynamics simulations and experiments. J. Mol. Biol375, 837-854 (2008).

Interlandi, G. Backbone conformations and side chain flexibility of two somatostatin mimics investigated by molecular dynamics simulations. Proteins: Structure, Function, Bioinformatics,  Epub ahead of print (2008).

Kolb, P., Kipouros, CB., Huang, D. & Caflisch, A. Structure-based tailoring of compound libraries for high-throughput screening: Discovery of novel EphB4 kinase inhibitors. Proteins 73, 11-18 (2008). 

Kolb, P., Huang, D., Dey, F. & Caflisch, A. Discovery of kinase inhibitors by high-throughput docking and  scoring based on a transferable linear interaction energy model. J. Med. Chem51, 1179-1188 (2008). 

Krivov, SV., Muff, S., Caflisch, A. & Karplus, M. One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process. J Phys Chem B. 112, 8701-8714 (2008).

Muff, S. & Caflisch, A. 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, 1185-1195 (2008).

Parmeggiani, F., Pellarin, R., Larsen, AP:, Varadamsetty, G., Stumpp, MT., Zerbe, O., Caflisch, A. & Plückthun, A. Designed Armadillo Repeat Proteins as general peptide-binding scaffolds: consensus design and computational optimization of hydrophobic core. J. Mol. Biol. 378, 1282-1304 (2008). 

Schenker, P., Alfarano, P., Kolb, P., Caflisch, A. & Baici, A. A double-headed cathepsin B inhibitor devoid of warhead. Protein Sci. 17, 2145-2155 (2008). 

Schuetz, P. & Caflisch, A. Efficient modularity optimization by multi-step greedy algorithm and vertex mover refinement. Phys. Rev. E 77, 046112 (2008).

Schuetz, P. & Caflisch, A. Multistep greedy algorithm identifies community structure in real-world and computer-generated networks. Phys. Rev. E 78, 026112 (2008).

Zhou, T., Huang, D. & Caflisch, A. Is quantum mechanics necessary for the predicting binding free energy? J. Med. Chem. 51, 4280-4288 (2008). 

Friedmann, R. & Caflisch, A. The protonation state of the catalytic aspartates in plasmepsin II. FEBS Lett. 581, 4120-4124 (2007).

Gfeller, D., De Los Rios, P., Caflisch,  A. & F. Rao. Complex network analysis of free-energy landscapes. PNAS U.S.A. 104,1817-1822 (2007).

Gorfe, A. & Caflisch, A. Ser170 controls the conformational multiplicity of the loop 166-175 in prion proteins: Implication for conversion and species barrier. FASEB J. 21, 3279-3287 (2007).

Pellarin, R., Guarnera, E. & Caflisch, A. Pathways and intermediates of amyloid fibril formation. J. Mol. Biol. 374, 917-924 (2007).

Rao, F., Settanni, G. & Caflisch A. Estimation of folding probabilities and phi values from molecular dynamics simulations of reversible Peptide folding. Methods Mol Biol. 350, 225-49 (2007).

Schroeder, V.,Vuissoz, J.M, Caflisch, A. & Kohler, H.P 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, 890-898 (2007).

Seeber, M., Cecchini, M., Rao, F., Settanni, G. & Caflisch, A. Wordom: a program for efficient analysis of molecular dynamics simulations. Bioinformatics 23, 2625-2627 (2007).

Tartaglia, G. &  Caflisch, A.. Computational analysis of the S. cerevisiae proteome reveals the function and cellular localization of the least and most amyloidogenic proteins. Proteins: Struct. Funct. Bioinf. 68, 273-278 (2007).

Caflisch, A. Computational models for the prediction of polypeptide aggregation propensity. Curr. Opin. Chemic. Biol. 10, 437-444 (2006).

Caflisch, A. Network and graph analyses of folding free energy surfaces. Curr. Opin. Struct. Biol. 16, 71-78 (2006).

Cecchini, M., Curcio, R., Pappalardo, M., Melki, R. & Caflisch, A. A molecular dynamics approach to the structural characterization of amyloid aggregation. J. Mol. Biol. 357, 1306-1321 (2006).

Huang, D., Luthi, U., Kolb, P., Cecchini, M., Barberis, A. & Caflisch, A. In silico discovery of beta-secretase inhibitors. J. Am. Chem. Soc. 128, 5436-5443 (2006).

Interlandi, G., Settanni, G. & Caflisch, A. Unfolding transition state and intermediates of the tumor suppressor p16INK4a investigated by molecular dynamics simulations. Proteins 64, 178-192 (2006). 

Kolb, P. & Caflisch, A. Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking. J. Med. Chem. 49, 7384-7392 (2006). 

Pellarin, R. & Caflisch,A. Interpreting the aggregation kinetics of amyloid peptides. J. Mol. Biol. 360, 882 - 892 (2006). 

Seeber, M., Fanelli, F., Paci, E. & Caflisch, A. Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane. Biophys. J. 91, 3276-3284 (2006).

Böckmann, R. A. & Caflisch, A. Spontaneous formation of detergent micelles around the outer membrane protein OmpX. Biophys. J. 88, 3191-3204 (2005).

Curcio, R., Caflisch, A. & Paci, E. Change of the unbinding mechanism upon a mutation: A molecular dynamics study of an antibody-hapten complex. Prot. Sci. 14, 2499-2514 (2005).

Gorfe, A. A. & Caflisch, A. Functional plasticity in the substrate binding site of beta-secretase. Structure 13, 1487-1498 (2005).  
Huang, D. Z., Luthi, U., Kolb, P., Edler, K., Cecchini, M., Audetat, S., Barberis, A. & Caflisch, A. Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations. J. Med. Chem. 48, 5108-5111 (2005).    

Muff, S., Rao, F. & Caflisch, A. Local modularity measure for network clusterizations. Phys. Rev. 72 (2005).  
Rao, F., Settanni, G., Guarnera, E. & Caflisch, A. Estimation of protein folding probability from equilibrium simulations. J. Chem. Phys. 122 (2005).

Settanni, G., Rao, F. & Caflisch, A. phi-Value analysis by molecular dynamics simulations of reversible folding. Proc. Natl. Acad. Sci. USA 102, 628-633 (2005).  

Tartaglia, G. G., Cavalli, A., Pellarin, R. & Caflisch, A. Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences. Prot. Sci. 14, 2723-2734 (2005).

Tartaglia, G. G., Pellarin, R., Cavalli, A. & Caflisch, A. Organism complexity anti-correlates with proteomic beta-aggregation propensity. Prot. Sci. 14, 2735-2740 (2005).

Caflisch, A. Protein folding: Simple models for a complex process. Structure 12, 1750-1752 (2004).

Cecchini, M., Kolb, P., Majeux, N. & Caflisch, A. Automated docking of highly flexible ligands by genetic algorithms: A critical assessment. J. Comput. Chem25, 412-422 (2004).

Cecchini, M., Rao, F., Seeber, M. & Caflisch, A. Replica exchange molecular dynamics simulations of amyloid peptide aggregation. J. Chem. Physics 121, 10748-10756 (2004).

Gorfe, A. A., Caflisch, A. & Jelesarov, I. The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: a molecular dynamics analysis.  J. Mol. Recognit. 17, 120-131 (2004).

Gorfe, A. A., Pellarin, R. & Caflisch, A. Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations. J. Am. Chem. Soc. 126, 15277-15286 (2004).

Huang, D. & Caflisch, A. Efficient evaluation of binding free energy using continuum electrostatics solvation. J. Med. Chem. 47, 5791-5797 (2004).

Levy, Y., Caflisch, A., Onuchic, J. N. & Wolynes, P. G. The folding and dimerization of HIV-1 protease: Evidence for a stable monomer from simulations. J. Mol. Biol. 340, 67-79 (2004).

Rao, F. & Caflisch, A. The protein folding network. J. Mol. Biol. 342, 299-306 (2004).

Settanni, G., Gsponer, J. & Caflisch, A. Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations. Biophys. J. 86, 1691-1701 (2004).    

Tartaglia, G. G., Cavalli, A., Pellarin, R. & Caflisch, A. The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates. Prot. Sci. 13, 1939-1941 (2004).