Amedeo Caflisch
Amedeo Caflisch
Department of Biochemistry, University of Zurich
Verified email at - Homepage
TitleCited byYear
CHARMM: the biomolecular simulation program
BR Brooks, CL Brooks III, AD Mackerell Jr, L Nilsson, RJ Petrella, B Roux, ...
Journal of computational chemistry 30 (10), 1545-1614, 2009
The protein folding network
F Rao, A Caflisch
Journal of molecular biology 342 (1), 299-306, 2004
Evaluation of a fast implicit solvent model for molecular dynamics simulations
P Ferrara, J Apostolakis, A Caflisch
Proteins: Structure, Function, and Bioinformatics 46 (1), 24-33, 2002
The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour
CN Kaiser‐Bunbury, S Muff, J Memmott, CB Müller, A Caflisch
Ecology letters 13 (4), 442-452, 2010
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
J Gsponer, U Haberthür, A Caflisch
Proceedings of the National Academy of Sciences 100 (9), 5154-5159, 2003
Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase
A Caflisch, A Miranker, M Karplus
Journal of medicinal chemistry 36 (15), 2142-2167, 1993
Interpreting the aggregation kinetics of amyloid peptides
R Pellarin, A Caflisch
Journal of molecular biology 360 (4), 882-892, 2006
Wordom: a program for efficient analysis of molecular dynamics simulations
M Seeber, M Cecchini, F Rao, G Settanni, A Caflisch
Bioinformatics 23 (19), 2625-2627, 2007
FACTS: Fast analytical continuum treatment of solvation
U Haberthür, A Caflisch
Journal of computational chemistry 29 (5), 701-715, 2008
PARP1 ADP-ribosylates lysine residues of the core histone tails
S Messner, M Altmeyer, H Zhao, A Pozivil, B Roschitzki, P Gehrig, ...
Nucleic acids research 38 (19), 6350-6362, 2010
Acid and thermal denaturation of barnase investigated by molecular dynamics simulations
A Caflisch, M Karplus
Journal of molecular biology 252 (5), 672-708, 1995
Predicting free energy changes using structural ensembles
A Benedix, CM Becker, BL de Groot, A Caflisch, RA Böckmann
Nature methods 6 (1), 3, 2009
Folding simulations of a three-stranded antiparallel β-sheet peptide
P Ferrara, A Caflisch
Proceedings of the National Academy of Sciences 97 (20), 10780-10785, 2000
Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases
F Rosenthal, KLH Feijs, E Frugier, M Bonalli, AH Forst, R Imhof, ...
Nature structural & molecular biology 20 (4), 502, 2013
Replica exchange molecular dynamics simulations of amyloid peptide aggregation
M Cecchini, F Rao, M Seeber, A Caflisch
The Journal of chemical physics 121 (21), 10748-10756, 2004
Prediction of aggregation rate and aggregation‐prone segments in polypeptide sequences
GG Tartaglia, A Cavalli, R Pellarin, A Caflisch
Protein Science 14 (10), 2723-2734, 2005
Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylketonuria
L Adler-Abramovich, L Vaks, O Carny, D Trudler, A Magno, A Caflisch, ...
Nature chemical biology 8 (8), 701, 2012
Efficient modularity optimization by multistep greedy algorithm and vertex mover refinement
P Schuetz, A Caflisch
Physical Review E 77 (4), 046112, 2008
Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water
J Apostolakis, P Ferrara, A Caflisch
The Journal of chemical physics 110 (4), 2099-2108, 1999
Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase.
A Caflisch, M Karplus
Proceedings of the National Academy of Sciences 91 (5), 1746-1750, 1994
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