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Department of Biochemistry

Publications Caflisch Group 1992-2003 (in alphabetical order)

Caflisch, A. Folding for binding or binding for folding? Trends Biotechnol21, 423-425 (2003).    

Cavalli, A., Haberthur, U., Paci, E. & Caflisch, A. Fast protein folding on downhill energy landscape. Prot. Sci12, 1801-1803 (2003).    

Gsponer, J., Haberthur, U. & Caflisch, A. The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35. Proc. Natl. Acad. Sci. USA 100, 5154-5159 (2003).    

Haberthur, U., Majeux, N., Werner, P. & Caflisch, A. Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution. J. Comput. Chem. 24, 1936-1949 (2003).  
Levy, Y. & Caflisch, A. Flexibility of monomeric and dimeric HIV-1 protease. J. Phys. Chem. 107, 3068-3079 (2003). 
Paci, E., Cavalli, A., Vendruscolo, M. & Caflisch, A. Analysis of the distributed computing approach applied to the folding of a small beta peptide. Proc. Natl. Acad. Sci. USA 100, 8217-8222 (2003).  
Rao, F. & Caflisch, A. Replica exchange molecular dynamics simulations of reversible folding. J. Chem. Physics 119, 4035-4042 (2003). 
Uk, B., Taufer, M., Stricker, T., Settanni, G., Cavalli, A. & Caflisch, A. in International Symposium on Cluster Computing and the Grid (CCGRID) (2003).  
Werner, P. & Caflisch, A. A sphere-based model for the electrostatics of globular proteins. J. Am. Chem. Soc. 125, 4600-4608 (2003).    

Cavalli, A., Ferrara, P. & Caflisch, A. Weak temperature dependence of the free energy surface and folding pathways of structured peptides. Proteins-Structure Function and Genetics 47, 305-314 (2002).  
Ferrara, P., Apostolakis, J. & Caflisch, A. Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins 46, 24-33 (2002). 
Gorfe, A. A., Ferrara, P., Caflisch, A., Marti, D. N., Bosshard, H. R. & Jelesarov, I. Calculation of protein ionization equilibria with conformational sampling: pK(a) of a model leucine zipper, GCN4 and barnase. Proteins 46, 41-60 (2002).    

Gsponer, J. & Caflisch, A. Molecular dynamics simulations of protein folding from the transition state. Proc. Natl. Acad. Sci. USA 99, 6719-6724 (2002). 
Taufer, M., Perathoner, E., Cavalli, A., Caflisch, A. & Stricker, T. in International Parallele and Distributed Processing Symposium (IPDPS) (2002). 

Ahmed, S., Majeux, N. & Caflisch, A. Hydrophobicity and functionality maps of farnesyltransferase. J. Mol. Graph. Mod. 19, 307-+ (2001). 
Budin, N., Ahmed, S., Majeux, N. & Caflisch, A. An evolutionary approach for structure-based design of natural and nonnatural peptidic ligands. Comb. Chem. High Throughput Screen 4, 661-673 (2001).    

Budin, N., Majeux, N. & Caflisch, A. Fragment-based flexible ligand docking by evolutionary optimization. Biol. Chem. 382, 1365-1372 (2001).
Budin, N., Majeux, N., Tenette-Souaille, C. & Caflisch, A. Structure-based ligand design by a build-up approach and genetic algorithm search in conformational space. J. Comput. Chem. 22, 1956-1970 (2001).
Ferrara, P. & Caflisch, A. Native topology or specific interactions: What is more important for protein folding? J. Mol. Biol. 306, 837-850 (2001).  
Gsponer, J. & Caflisch, A. Role of native topology investigated by multiple unfolding simulations of four SH3 domains. J. Mol. Biol. 309, 285-298 (2001).  
Gsponer, J., Ferrara, P. & Caflisch, A. Flexibility of the murine prion protein and its Asp178Asn mutant investigated by molecular dynamics simulations. J. Mol. Graph. Mod. 20, 169-182 (2001).    

Majeux, N., Scarsi, M. & Caflisch, A. Efficient electrostatic solvation model for protein-fragment docking. Proteins 42, 256-268 (2001).    

Paci, E., Caflisch, A., Pluckthun, A. & Karplus, M. Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study. J. Mol. Biol. 314, 589-605 (2001).

Caflisch, A., Schramm, H. J. & Karplus, M. Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach. J. Comput. Aided Mol. Des. 14, 161-179 (2000).    
Ferrara, P., Apostolakis, J. & Caflisch, A. Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations. J. Phys. Chem. 104, 5000-5010 (2000).    
Ferrara, P., Apostolakis, J. & Caflisch, A. Targeted molecular dynamics simulations of protein unfolding. J. Phys. Chem. 104, 4511-4518 (2000).    
Ferrara, P., Apostolakis, J. & Caflisch, A. Computer simulations of protein folding by targeted molecular dynamics. Proteins 39, 252-260 (2000).    
Ferrara, P. & Caflisch, A. Folding simulations of a three-stranded antiparallel beta-sheet peptide. Proc. Natl. Acad. Sci. USA 97, 10780-10785 (2000).    
Hiltpold, A., Ferrara, P., Gsponer, J. & Caflisch, A. Free energy surface of the helical peptide Y(MEARA)(6). J. Phys. Chem. 104, 10080-10086 (2000).    
Majeux, N., Scarsi, M., Tenette-Souaille, C. & Caflisch, A. Hydrophobicity maps and docking of molecular fragments with solvation. Perspectives in Drug Discovery and Design 20, 145-169 (2000).    
Apostolakis, J. & Caflisch, A. Computational ligand design. Comb. Chem. High Throughput Screen. 2, 91-104 (1999).    
Apostolakis, J., Ferrara, P. & Caflisch, A. Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water. J. Chem. Phys. 110, 2099-2108 (1999).    
Caflisch, A. & Karplus, M. Structural details of urea binding to barnase: a molecular dynamics analysis. Structure 7, 477-488 (1999).    
Galzitskaya, O. & Caflisch, A. Solution conformation of phakellistatin 8 investigated by molecular dynamics simulations. J. Mol. Graph. Model. 17, 19-27 (1999).    
Majeux, N., Scarsi, M., Apostolakis, J., Ehrhardt, C. & Caflisch, A. Exhaustive docking of molecular fragments with electrostatic solvation. Proteins 37, 88-105 (1999).    
Scarsi, M. & Caflisch, A. Comment on the validation of continuum electrostatics models. J. Comput. Chem20, 1533-1536 (1999).    
Scarsi, M., Majeux, N. & Caflisch, A. Hydrophobicity at the surface of proteins. Proteins 37, 565-575 (1999).  

Apostolakis, J., Pluckthun, A. & Caflisch, A. Docking small ligands in flexible binding sites. J. Comput. Chem. 19, 21-37 (1998).    
Caflisch, A., Walchli, R. & Ehrhardt, C. Computer-aided design of thrombin inhibitors. News Pysiol. Sci. 13, 182-189 (1998).    
Scarsi, M., Apostolakis, J. & Caflisch, A. Comparison of a GB solvation model with explicit solvent simulations: Potentials of mean force and conformational preferences of alanine dipeptide and 1,2-dichloroethane. J. Phys. Chem. 102, 3637-3641 (1998).    
Caflisch, A., Fischer, S. & Karplus, M. Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP-substrate complex. J. Comput. Chem18, 723-743 (1997).    
Scarsi, M., Apostolakis, J. & Caflisch, A. Continuum electrostatic energies of macromolecules in aqueous solutions. J. Phys. Chem. 101, 8098-8106 (1997). 

Caflisch, A. Computational combinatorial ligand design: Application to human alpha-thrombin. J. Comp. Aidel Mol. Design 10, 372-396 (1996).    
Caflisch, A. & Karplus, M. Computational combinatorial chemistry for de novo ligand design: Review and assessment. Perspectives in Drug Discovery and Design 3, 51-84 (1995).    
Caflisch, A. & Karplus, M. Acid and Thermal-Denaturation of Barnase Investigated by Molecular-Dynamics Simulations. J. Mol. Biol. 252, 672-708 (1995).    
Caflisch, A. & Karplus, M. Molecular-Dynamics Simulation of Protein Denaturation - Solvation of the Hydrophobic Cores and Secondary Structure of Barnase. Proc. Natl. Acad. Sci. USA 91, 1746-1750 (1994). 

Caflisch, A., Miranker, A. & Karplus, M. Multiple Copy Simultaneous Search and Construction of Ligands in Binding-Sites - Application to Inhibitors of Hiv-1 Aspartic Proteinase. J. Med. Chem. 36, 2142-2167 (1993).    
Caflisch, A., Niederer, P. & Anliker, M. Monte-Carlo Minimization with Thermalization for Global Optimization of Polypeptide Conformations in Cartesian Coordinate Space. Proteins 14, 102-109 (1992).    
Caflisch, A., Niederer, P. & Anliker, M. Monte-Carlo Docking of Oligopeptides to Proteins. Proteins 13, 223-230 (1992).