Caflisch, Amedeo - Department of Biochemistry, Universit�t Z�rich

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Caflisch, Amedeo - Department of Biochemistry, Universit�t Z�rich

Local modularity measure for network clusterizations Stefanie Muff, Francesco Rao, and Amedeo Caflisch
Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water
One-Dimensional Barrier Preserving Free-Energy Projections of a -sheet Miniprotein: New Insights into the Folding Process
The Chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 Is Essential for H3K27me3 Binding and
Supporting Information Kinase selectivity potential for inhibitors targeting the ATP
Complex network analysis of free-energy landscapes SUPPLEMENTARY MATERIAL
ETNA: Equilibrium transitions network and Arrhenius equation for extracting folding kinetics from REMD simulations
Extracting Physically Intuitive Reaction Coordinates from Transition Networks of a -Sheet Miniprotein
-Value analysis by molecular dynamics simulations of reversible folding
Activation of the West Nile virus NS3 protease: Molecular dynamics evidence
Comment on the Validation of Continuum Electrostatics Models
Biophysical Journal, Volume 97 Supporting Material
Activation of the West Nile virus NS3 protease: Molecular dynamics evidence for a conformational selection mechanism
Slow Folding of Cross-Linked r-Helical Peptides Due to Steric Hindrance B. Paoli, R. Pellarin, and A. Caflisch*
FOR THE RECORD Organism complexity anti-correlates with proteomic
Docking Small Ligands in Flexible Binding Sites
Weak Temperature Dependence of the Free Energy Surface and Folding Pathways of Structured Peptides
2142 J. Med. Chem. 1993,36, 2142-2167 Multiple Copy Simultaneous Search and Construction of Ligands in Binding Sites
Free Energy Surfaces from Single-Distance Information Philipp Schuetz,
Calculation of Protein Ionization Equilibria With Conformational Sampling: pKa of a Model
Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways
Designed Armadillo Repeat Proteins as General Peptide Binding Scaffolds: Consensus Design and Computational
Supporting Information NMR study of complexes between low-molecular weight inhibitors and the
J. Mol. Biol. (1995) 252, 672708 Acid and Thermal Denaturation of Barnase
Molecular dynamics simulations of protein folding from the transition state
Factor XIII activation peptide is released into plasma upon cleavage by thrombin and shows a different structure compared
CHARMM: The Biomolecular Simulation Program B. R. BROOKS,1* C. L. BROOKS III,2,3* A. D. MACKERELL, Jr.,4* L. NILSSON,5* R. J. PETRELLA,6,7* B. ROUX,8* Y. WON,9*
10.1110/ps.037341.108Access the most recent version at doi: 2008 17: 2145-2155; originally published online Sep 16, 2008;Protein Sci.
Automated Docking of Highly Flexible Ligands by Genetic Algorithms: A Critical Assessment
Discovery of Kinase Inhibitors by High-Throughput Docking and Scoring Based on a Transferable Linear Interaction Energy Model
Native Topology or Specific Interactions: What is More Important for Protein Folding?
Membrane Localization and Flexibility of a Lipidated Ras Peptide Studied by Molecular Dynamics Simulations
FOR THE RECORD Fast protein folding on downhill energy landscape
Multistep greedy algorithm identifies community structure in real-world and computer-generated networks
Micelle-Like Architecture of the Monomer Ensemble of Alzheimer's Amyloid-Peptide in Aqueous Solution and
arXiv:q-bio/0409021v1[q-bio.BM]17Sep2004 Replica exchange molecular dynamics simulations of amyloid peptide aggregation
Performance Characterization of a Molecular Dynamics Code on PC Clusters Is there any easy parallelism in CHARMM?
The robustness of pollination networks to the loss of species and interactions: a quantitative approach
PARP1 ADP-ribosylates lysine residues of the core histone tails
Supporting Material for: Soluble protofibrils are metastable intermediates in simulations of
r XXXX American Chemical Society 471 DOI: 10.1021/jz900318t |J. Phys. Chem. Lett. 2010, 1, 471474 pubs.acs.org/JPCL
How Does a Simplified-Sequence Protein Fold? Enrico Guarnera, Riccardo Pellarin, and Amedeo Caflisch*
Perspectives in Drug Discovery and Design, 20: 145169, 2000. KLUWER/ESCOM
Journal of Molecular Graphics and Modelling 20 (2001) 169182 Flexibility of the murine prion protein and its Asp178Asn mutant
pubs.acs.org/jmcPublished on Web 09/29/2009r 2009 American Chemical Society J. Med. Chem. 2009, 52, 64336446 6433
proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS On the orientation of the catalytic
Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Danzhi Huang and Amedeo Caflisch*
Supplementary Material Estimation of protein folding probability from equilibrium
Support Information High-throughput Virtual Screening using Quantum
Amyloid Fibril Polymorphism Is under Kinetic Control Riccardo Pellarin, Philipp Schuetz,
FOR THE RECORD The role of aromaticity, exposed surface, and dipole moment
Supplementary Material A Molecular Dynamics Approach to the Structural
Targeted Molecular Dynamics Simulations of Protein Unfolding Philippe Ferrara, Joannis Apostolakis, and Amedeo Caflisch*
Flexibility of Monomeric and Dimeric HIV-1 Protease Yaakov Levy*,, and Amedeo Caflisch*,|
Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions Marco Scarsi, Joannis Apostolakis, and Amedeo Caflisch*
High-throughput Virtual Screening using Quantum Mechanical Probes
Appendix S1. Plant species extinction patterns following animal extinction scenarios of systematic removal from the strongest interactor and systematic removal from the weakest
Vol. 23 no. 19 2007, pages 26252627 BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btm378
COMMUNICATION Pathways and Intermediates of Amyloid Fibril Formation
Efficient modularity optimization by multistep greedy algorithm and vertex mover refinement Philipp Schuetz and Amedeo Caflisch
r XXXX American Chemical Society 3027 DOI: 10.1021/jz100967z |J. Phys. Chem. Lett. 2010, 1, 30273032 pubs.acs.org/JPCL
Supplementary Material of manuscript: "-Value analysis by molecular dynamics simulations of re-
Crowding Effects on Amyloid Aggregation Kinetics Supplementary Materials
Network and graph analyses of folding free energy surfaces Amedeo Caflisch
The slow folding of cross-linked -helical peptides is due to steric SUPPLEMENTARY MATERIAL
DOI: 10.1002/cmdc.200900078 Discovery of Plasmepsin Inhibitors by Fragment-Based
Designed Armadillo Repeat Proteins as General Peptide-Binding Scaffolds: Consensus Design and
Supplementary Information Riccardo Pellarin and Amedeo Caflisch
The Folding and Dimerization of HIV-1 Protease: Evidence for a Stable Monomer from Simulations
Evaluation of a Fast Implicit Solvent Model for Molecular Dynamics Simulations
Folding for binding or binding for folding? Amedeo Caflisch
nature methods | VOL.6 NO.1 | JANUARY 2009 | 3 correspondence
Fragment-Based Flexible Ligand Docking by Evolutionary Optimization
SUPPLEMENTAL ONLINE MATERIAL1 FIGURE LEGENDS2
Computer Simulations of Protein Folding by Targeted Molecular Dynamics
Supporting Information 1 FESST application to atomistic simulations of -sheet folding 4
Supplementary Information Discovery of cell-permeable nonpeptide inhibitors of
2D-IR Study of a Photoswitchable Isotope-Labeled r-Helix Ellen H. G. Backus,,
The FASEB Journal Research Communication Ser170 controls the conformational multiplicity of the
The Protein Folding Network Francesco Rao and Amedeo Caflisch*
Characterization and further stabilization of designed ankyrin repeat proteins by combining molecular
Forces and Energetics of Hapten-Antibody Dissociation: A Biased Molecular Dynamics
Supporting Information The free energy landscape of small molecule
Supporting Information Ihalainen et al. 10.1073/pnas.0712099105
9,10-Anthraquinone hinders b-aggregation: How does a small
Supplementary Material for: The Protonation State of the Catalytic Aspartates in Plasmepsin II
One-Dimensional Barrier-Preserving Free-Energy Projections of a -sheet Miniprotein: New Insights into the Folding Process
Supplemental Table S1. Identification codes and source of 29 putative inhibitors of human cathepsin B. The ZINC-codes are those of the database 2005 [Irwin, J. J., and
Amyloid Aggregation on Lipid Bilayers and Its Impact on Membrane Permeability
Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences
Complementing Ultrafast Shape Recognition with an Optical Isomerism Descriptor
Computational Analysis of the S. cerevisiae Proteome Reveals the Function and Cellular Localization of the
The Free Energy Landscape of Small Molecule Unbinding Danzhi Huang, Amedeo Caflisch*
Software News and Updates Wordom: A User-Friendly Program for the Analysis of
Published: April 25, 2011 r 2011 American Chemical Society 6358 dx.doi.org/10.1021/jp2014918 |J. Phys. Chem. B 2011, 115, 63586365
Received: 2 April 2009, Revised: 7 July 2009, Accepted: 15 July 2009, Published online in Wiley InterScience: 2009 Library screening by fragment-based docking
Quantum Mechanical Methods for Drug Design Ting Zhou, Danzhi Huang, and Amedeo Caflisch
BIOINFORMATICS ORIGINAL PAPER Vol. 26 no. 2 2010, pages 198204
Epigenetic mechanisms regulate stage differentiation in the minimized protozoan Giardia lambliammi_7062 1..20
Supplementary Methods Cell culture, transfection of siRNA and overexpression of PARP1
Complete Phenotypic Recovery of an Alzheimer's Disease Model by a Quinone-Tryptophan Hybrid
IL, IID III IV VIII VIIII X
Journal of Molecular Graphics and Modelling 29 (2010) 443449 Contents lists available at ScienceDirect
Amyloid fibril polymorphism is under kinetic control
A Gain-of-Function Mutation of Arabidopsis CRYPTOCHROME1 Promotes Flowering1[W][OA]
Subscriber access provided by UNIV ZURICH The Journal of Physical Chemistry B is published by the American Chemical
Supplementary Information for: Amyloid Aggregation on Lipid Bilayers and its Impact on Membrane
Subscriber access provided by UNIV ZURICH Journal of Chemical Information and Modeling is published by the American
Data Management System for Distributed Virtual Supporting Information
Discovery of a Non-Peptidic Inhibitor of West Nile Virus NS3 Protease by High-Throughput Docking
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
Identification of the protein folding transition state from molecular dynamics trajectories
Identification of the protein folding transition state from molecular dynamics trajectories
SupplementaryMaterials Table1S.TimedependentpropertiesinCORREL.
pubs.acs.org/jmc Published on Web 07/02/2009 r 2009 American Chemical Society 4860 J. Med. Chem. 2009, 52, 48604868
Supporting Information Flaviviral protease inhibitors identied by fragment-based
A fluorescence quenching assay to discriminate between specific and nonspecific inhibitors of dengue virus protease
Bodenreider et al Supporting Information
Supporting Information StructureBased Optimization of Potent and Selective Inhibitors of the
proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Kinetic analysis of molecular dynamics
FACTS: Fast Analytical Continuum Treatment of Solvation
Characterization and Further Stabilization of Designed Ankyrin Repeat Proteins by Combining Molecular
Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear
Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization Fabian Dey and Amedeo Caflisch*
Fragment-based de novo ligand design by multi-objective evolutionary optimization.
proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Structure-based tailoring of compound
Structure-based tailoring of compound libraries for high-throughput screening: Discovery of novel
Supplementary Material for: Pepsinogen-like activation intermediate of plasmepsin II revealed by
Is Quantum Mechanics Necessary for Predicting Binding Free Energy? Ting Zhou, Danzhi Huang,* and Amedeo Caflisch*
Supporting Information Is quantum mechanics necessary for predicting
-Helix folding in the presence of structural constraints
Supplementary Material for: The multistep greedy algorithm identifies community structure in
SUPPLEMENTARY MATERIAL Ser170 Controls the Conformational Multiplicity of the Loop 166-175 in Prion Proteins
The protonation state of the catalytic aspartates in plasmepsin II Ran Friedman*, Amedeo Caflisch*
From: Methods in Molecular Biology, vol. 350: Protein Folding Protocols Edited by: Y. Bai and R. Nussinov Humana Press Inc., Totowa, NJ
Complex network analysis of free-energy landscapes , P. De Los Rios
Unfolding Transition State and Intermediates of the Tumor Suppressor p16INK4a
Unfolding transition state and intermediates of the tumor suppressor
In Silico Discovery of -Secretase Inhibitors Danzhi Huang, Urs Luthi, Peter Kolb, Marco Cecchini, Alcide Barberis, and
Supporting Information In silico discovery of -secretase inhibitors
Interpreting the Aggregation Kinetics of Amyloid Peptides
Sequential Unfolding of Individual Helices of Bacterioopsin Observed in Molecular Dynamics Simulations of Extraction from the Purple Membrane
Computational models for the prediction of polypeptide aggregation propensity
Automatic and Efficient Decomposition of Two-Dimensional Structures of Small Molecules for Fragment-Based High-Throughput Docking
A Molecular Dynamics Approach to the Structural Characterization of Amyloid Aggregation
Spontaneous Formation of Detergent Micelles around the Outer Membrane Protein OmpX
Estimation of protein folding probability from equilibrium simulations Francesco Rao, Giovanni Settanni, Enrico Guarnera, and Amedeo Caflischa
Discovery of Cell-Permeable Non-Peptide Inhibitors of -Secretase by
Change of the unbinding mechanism upon a mutation: A molecular dynamics study
Molecular Dynamics Simulations to Study Protein Folding and Unfolding
Supplementary Material Averageclusteringcoefficient
Doublie , S., Sawaya, M.R., and Ellenberger, T. (1999). Struct. Fold.son and Beese, 2004). The same mispair, on the other Des. 7, R31R35.hand, is poorly extended by Dpo4: it was shown to form
A Sphere-Based Model for the Electrostatics of Globular Philipp Werner and Amedeo Caflisch*
The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an
Analysis of the distributed computing approach applied to the folding of a small peptide
Efficient Evaluation of the Effective Dielectric Function of a Macromolecule in Aqueous Solution
Replica exchange molecular dynamics simulations of reversible folding Francesco Rao and Amedeo Caflischa)
Efficient Electrostatic Solvation Model for Protein-Fragment Docking
Hydrophobicity and functionality maps of farnesyltransferase
Role of Native Topology Investigated by Multiple Unfolding Simulations of Four SH3 Domains
Combinatorial Chemistry & High Throughput Screening, 2001, 4, 661-673 661 AnEvolutionaryApproachfor Structure-based Design of Natural and Non-
Structure-Based Ligand Design by a Build-Up Approach and Genetic Algorithm
Journal of Computer-Aided Molecular Design, 14: 161179, 2000. KLUWER/ESCOM
Folding simulations of a three-stranded antiparallel -sheet peptide
Free Energy Surface of the Helical Peptide Y(MEARA)6 Andre Hiltpold, Philippe Ferrara, Jo1rg Gsponer, and Amedeo Caflisch*
Thermodynamics and Kinetics of Folding of Two Model Peptides Investigated by Molecular Dynamics Simulations
Exhaustive Docking of Molecular Fragments With Electrostatic Solvation
Hydrophobicity at the Surface of Proteins Marco Scarsi, Nicolas Majeux, and Amedeo Caflisch*
Concluding remarks As long as crystals of the entire channel mol-
Comparison of a GB Solvation Model with Explicit Solvent Simulations: Potentials of Mean Force and Conformational Preferences of Alanine Dipeptide and 1,2-Dichloroethane
Docking by Monte Carlo Minimization with a Solvation Correction: Application
Supporting Information Discovery of a non-peptidic inhibitor of West Nile virus NS3
Formation of the Folding Nucleus of an SH3 Domain Investigated by Loosely Coupled Molecular Dynamics Simulations
NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2BNS3 protease
DOI: 10.1002/cmdc.201100237 Small Molecule Binding to Proteins: Affinity and Binding/Unbinding
structural communications 842 doi:10.1107/S1744309111018604 Acta Cryst. (2011). F67, 842850
Supporting Information Copyright Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, 2011
Published: September 05, 2011 r 2011 American Chemical Society 1265 dx.doi.org/10.1021/cb200103h |ACS Chem. Biol. 2011, 6, 12651276
Dynamics in the Active Site of -Secretase: A Network Analysis of Atomistic Simulations
Published: September 23, 2011 r 2011 American Chemical Society 13065 dx.doi.org/10.1021/jp2076935 |J. Phys. Chem. B 2011, 115, 1306513074
Structural Basis for Inhibiting ----Amyloid Oligomerization by a Non-Coded -Breaker Substituted Endomorphin Analogue
Supporting Material for: Surfactant effects on amyloid aggregation kinetics
Surfactant Effects on Amyloid Aggregation Kinetics Ran Friedman 1, 2
Disordered Binding of Small Molecules to A (1228)*S Received for publication,July 25, 2011, and in revised form, September 23, 2011 Published, JBC Papers in Press,October 3, 2011, DOI 10.1074/jbc.M111.285957
DISORDERED BINDING OF SMALL MOLECULES TO A12-28 Marino Convertino, Andreas Vitalis*
Hydrogen Bonding Penalty upon Ligand Binding Hongtao Zhao, Danzhi Huang*
Supporting information for: Dynamics in the active site of -secretase: A network analysis of atomistic
4 Current Physical Chemistry, 2012, 2, 4-11 1877-9468/12 $58.00+.00 2012 Bentham Science Publishers