Amedeo Caflisch

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Francesco Raozurich or rome or strasbourg or freiburgVerified email at frias.uni-freiburg.de
Stefanie MuffNorwegian University of Science and TechnologyVerified email at ntnu.no
Andreas VitalisUniversity of ZurichVerified email at bioc.uzh.ch
Hongtao ZhaoVerified email at lephar.com
Peter KolbPhilipps-University MarburgVerified email at uni-marburg.de
Giovanni SettanniPhysics Department, JG University MainzVerified email at uni-mainz.de
Andrea CavalliUniversity of Cambridge, UK. IRB Bellinzona, SwitzerlandVerified email at irb.usi.ch
Ran FriedmanLinnæus University, Kalmar, SwedenVerified email at lnu.se
Dimitrios SpiliotopoulosXenometrix AGVerified email at xenometrix.ch
Marco CecchiniAssistant Professor, University of StrasbourgVerified email at unistra.fr
Andreas PluckthunBiochemisches Institut, Universität ZürichVerified email at bioc.uzh.ch
Ehud GazitTel Aviv University, IsraelVerified email at tauex.tau.ac.il
Marino ConvertinoParion SciencesVerified email at parion.com
Michele SeeberUniversity of Modena and Reggio EmiliaVerified email at unimore.it
Emanuele PaciUniversity of LeedsVerified email at leeds.ac.uk
gian gaetano tartagliaIIT & Sapienza (CRG / ICREA / University of Cambridge / University of Zurich)Verified email at iit.it
Jean-Rémy MarchandComputational chemist, CADD group, Novartis NIBRVerified email at novartis.com
Oliver ZerbeUniversity of Zurich, Department of ChemistryVerified email at chem.uzh.ch
Enrico GuarneraComputational Structural Biology @ Merck KGaAVerified email at merckgroup.com
Peter HammDepartment of Chemistry, University of ZurichVerified email at chem.uzh.ch

Amedeo Caflisch

Department of Biochemistry, University of Zurich

Verified email at bioc.uzh.ch - Homepage

Molecular dynamics drug design


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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	7076	2009
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	455	2010
The protein folding network F Rao, A Caflisch Journal of molecular biology 342 (1), 299-306, 2004	415	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	355	2002
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), 701-706, 2012	326	2012
Protein structure-based drug design: from docking to molecular dynamics P Śledź, A Caflisch Current opinion in structural biology 48, 93-102, 2018	320	2018
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	307	2003
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), 502-507, 2013	294	2013
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	278	2007
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	277	2010
Interpreting the aggregation kinetics of amyloid peptides R Pellarin, A Caflisch Journal of molecular biology 360 (4), 882-892, 2006	270	2006
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	258	1993
Predicting free energy changes using structural ensembles A Benedix, CM Becker, BL de Groot, A Caflisch, RA Böckmann Nature methods 6 (1), 3-4, 2009	245	2009
FACTS: Fast analytical continuum treatment of solvation U Haberthür, A Caflisch Journal of computational chemistry 29 (5), 701-715, 2008	238	2008
Wordom: a user‐friendly program for the analysis of molecular structures, trajectories, and free energy surfaces M Seeber, A Felline, F Raimondi, S Muff, R Friedman, F Rao, A Caflisch, ... Journal of computational chemistry 32 (6), 1183-1194, 2011	233	2011
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	221	2004
Efficient modularity optimization by multistep greedy algorithm and vertex mover refinement P Schuetz, A Caflisch Physical Review E 77 (4), 046112, 2008	220	2008
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	216	2005
Acid and thermal denaturation of barnase investigated by molecular dynamics simulations A Caflisch, M Karplus Journal of molecular biology 252 (5), 672-708, 1995	211	1995
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	206	2000

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