Publications of the Caflisch group

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 B. 113, 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. Chem. 29, 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. Biol. 375, 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. Chem. 51, 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).