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Lista de obras de Amedeo Caflisch

2D-IR study of a photoswitchable isotope-labeled alpha-helix.

artículo científico publicado en 2010

50 Years of Lifson-Roig Models: Application to Molecular Simulation Data

artículo científico publicado en 2011

9,10-Anthraquinone hinders beta-aggregation: how does a small molecule interfere with Abeta-peptide amyloid fibrillation?

artículo científico publicado en 2009

A Reader-Based Assay for m6A Writers and Erasers

artículo científico publicado en 2019

A Small-Molecule Inhibitor of Lin28.

artículo científico publicado en 2016

A combined NMR and computational approach to investigate peptide binding to a designed Armadillo repeat protein

artículo científico publicado en 2015

A double-headed cathepsin B inhibitor devoid of warhead

artículo científico publicado en 2008

A fluorescence quenching assay to discriminate between specific and nonspecific inhibitors of dengue virus protease.

artículo científico publicado en 2009

A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods

artículo científico publicado en 2014

A sphere-based model for the electrostatics of globular proteins

article

Activation of the West Nile virus NS3 protease: Molecular dynamics evidence for a conformational selection mechanism

artículo científico publicado en 2009

Alpha-Helix folding in the presence of structural constraints.

artículo científico publicado en 2008

Amyloid aggregation on lipid bilayers and its impact on membrane permeability.

artículo científico publicado en 2008

Amyloid fibril polymorphism is under kinetic control

artículo científico publicado en 2010

Amyloid β Fibril Elongation by Monomers Involves Disorder at the Tip.

artículo científico publicado en 2017

An ABSINTH-Based Protocol for Predicting Binding Affinities Between Proteins and Small Molecules

artículo científico publicado en 2020

Assessment of the fragment docking program SEED

artículo científico publicado en 2020

Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m<sup>6</sup>A) Recognition by the Reader Domain of YTHDC1

artículo científico publicado en 2021

Automated docking of highly flexible ligands by genetic algorithms: a critical assessment.

artículo científico publicado en 2004

Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking

artículo científico publicado en 2006

Binding Mode of Acetylated Histones to Bromodomains: Variations on a Common Motif

artículo científico

Binding Motifs in the CBP Bromodomain: An Analysis of 20 Crystal Structures of Complexes with Small Molecules

scientific article published on 08 August 2018

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

artículo científico publicado en 2009

Calculation of protein ionization equilibria with conformational sampling: pK(a) of a model leucine zipper, GCN4 and barnase

artículo científico publicado en 2002

Carnosine inhibits Aβ(42) aggregation by perturbing the H-bond network in and around the central hydrophobic cluster

artículo científico publicado en 2013

Characterization and further stabilization of designed ankyrin repeat proteins by combining molecular dynamics simulations and experiments

artículo científico publicado en 2007

Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple).

artículo científico publicado en 2018

Complementing ultrafast shape recognition with an optical isomerism descriptor ⬇️

artículo científico publicado el 29 de septiembre de 2010

Complete phenotypic recovery of an Alzheimer's disease model by a quinone-tryptophan hybrid aggregation inhibitor

artículo científico publicado en 2010

Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition

artículo científico publicado en 2016

Current kinase inhibitors cover a tiny fraction of fragment space.

artículo científico publicado en 2015

Data management system for distributed virtual screening

artículo científico publicado en 2009

Data publication with the structural biology data grid supports live analysis

artículo científico publicado en 2016

Delineation of folding pathways of a β-sheet miniprotein

artículo científico publicado en 2011

Derivatives of 3-amino-2-methylpyridine as BAZ2B Bromodomain Ligands: in silico Discovery and in crystallo Validation

artículo científico publicado en 2016

Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core

artículo científico publicado en 2007

Discovery of BAZ2A Bromodomain Ligands

Discovery of BAZ2A bromodomain ligands.

artículo científico publicado en 2017

Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking

artículo científico publicado en 2014

Discovery of CREBBP Bromodomain Inhibitors by High-Throughput Docking and Hit Optimization Guided by Molecular Dynamics

artículo científico publicado en 2016

Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking.

artículo científico publicado en 2017

Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics.

artículo científico publicado en 2013

Discovery of a Non-Peptidic Inhibitor of West Nile Virus NS3 Protease by High-Throughput Docking

artículo científico publicado en 2009

Discovery of a Novel Chemotype of Tyrosine Kinase Inhibitors by Fragment-Based Docking and Molecular Dynamics

artículo científico publicado en 2012

Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations

artículo científico publicado en 2005

Discovery of dual ZAP70 and Syk kinases inhibitors by docking into a rare C-helix-out conformation of Syk.

artículo científico publicado en 2014

Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model

artículo científico publicado en 2008

Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring

artículo científico publicado en 2009

Discovery of tyrosine kinase inhibitors by docking into an inactive kinase conformation generated by molecular dynamics.

artículo científico publicado en 2012

Disorder at the Tips of a Disease-Relevant Aβ42 Amyloid Fibril: A Molecular Dynamics Study

artículo científico publicado en 2018

Disordered binding of small molecules to Aβ(12-28).

artículo científico publicado en 2011

Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric

scientific article published on 20 July 2012

Disulfide bridge formation influences ligand recognition by the ATAD2 bromodomain

artículo científico publicado en 2018

Does bromodomain flexibility influence histone recognition?

artículo científico publicado en 2013

Dynamic microfluidic control of supramolecular peptide self-assembly

artículo científico publicado en 2016

Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories

artículo científico publicado en 2012

Efficient evaluation of binding free energy using continuum electrostatics solvation

artículo científico publicado en 2004

Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution ⬇️

artículo científico publicado el 30 de noviembre de 2003

Efficient modularity optimization by multistep greedy algorithm and vertex mover refinement.

artículo científico publicado en 2008

Estimation of folding probabilities and phi values from molecular dynamics simulations of reversible Peptide folding

artículo científico publicado en 2007

Estimation of protein folding probability from equilibrium simulations

artículo científico publicado en 2005

Evaluation of a fast implicit solvent model for molecular dynamics simulations

artículo científico publicado en 2002

Evolutionary conserved Tyr169 stabilizes the β2-α2 loop of the prion protein

artículo científico publicado en 2015

Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein

artículo científico publicado en 2010

Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics

artículo científico publicado en 2009

Flexible Binding of m6A Reader Protein YTHDC1 to Its Preferred RNA Motif

scientific article published on 14 November 2019

Focused conformational sampling in proteins.

artículo científico publicado en 2017

Fragment-Based Design of Selective Nanomolar Ligands of the CREBBP Bromodomain

artículo científico publicado en 2015

Fragment-based de novo ligand design by multiobjective evolutionary optimization

artículo científico publicado en 2008

Fragment-based docking: development of the CHARMMing Web user interface as a platform for computer-aided drug design

artículo científico publicado en 2014

Fragment-based in silico screening of bromodomain ligands

artículo científico publicado en 2016

Free Energy Guided Sampling

scientific article published on 04 May 2012

Free Energy Guided Sampling

artículo científico publicado en 2012

Free Energy Surfaces from Single-Distance Information

article

High-Throughput Fragment Docking into the BAZ2B Bromodomain: Efficient in Silico Screening for X-Ray Crystallography

artículo científico publicado en 2016

High-resolution visualisation of the states and pathways sampled in molecular dynamics simulations

artículo científico publicado en 2014

High-throughput virtual screening using quantum mechanical probes: discovery of selective kinase inhibitors

artículo científico publicado en 2010

Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers

scientific article published on 30 June 2020

How Does Darunavir Prevent HIV-1 Protease Dimerization?

artículo científico publicado en 2012

How does a simplified-sequence protein fold?

artículo científico publicado en 2009

In Silico Identification of JMJD3 Demethylase Inhibitors

artículo científico publicado en 2018

In silico discovery of beta-secretase inhibitors

artículo científico publicado en 2006

In silico fragment-based drug design with SEED

scientific article published on 17 July 2018

In silicoidentification and crystal structure validation of caspase-3 inhibitors without a P1 aspartic acid moiety ⬇️

artículo científico publicado el 13 de julio de 2011

Interpreting the aggregation kinetics of amyloid peptides

scientific article published on 05 June 2006

Is quantum mechanics necessary for predicting binding free energy?

artículo científico publicado en 2008

Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis

artículo científico publicado en 2009

Kinetic Control of Amyloidogenesis Calls for Unconventional Drugs To Fight Alzheimer's Disease

artículo científico publicado en 2020

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

artículo científico publicado en 2008

Kinetic response of a photoperturbed allosteric protein

artículo científico publicado en 2013

Ligand retargeting by binding site analogy

scientific article published on 25 April 2019

Local modularity measure for network clusterizations

scientific article published on 07 November 2005

Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases.

artículo científico publicado en 2013

Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations

artículo científico publicado en 2004

Methylations of tryptophan-modified naphthoquinone affect its inhibitory potential toward Aβ aggregation

artículo científico publicado en 2013

Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-β peptide in aqueous solution and its implications for Aβ aggregation

artículo científico publicado en 2010

Molecular dynamics in drug design.

artículo científico publicado en 2014

Multistep greedy algorithm identifies community structure in real-world and computer-generated networks.

artículo científico publicado en 2008

N,N Dimethylacetamide a drug excipient that acts as bromodomain ligand for osteoporosis treatment

artículo científico publicado en 2017

NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease

artículo científico publicado en 2009

New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow

artículo científico publicado en 2013

On the orientation of the catalytic dyad in aspartic proteases

artículo científico publicado en 2010

On the removal of initial state bias from simulation data

artículo científico publicado en 2019

One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process

artículo científico publicado en 2008

Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy

artículo científico publicado en 2012

Optimization of inhibitors of the tyrosine kinase EphB4. 2. Cellular potency improvement and binding mode validation by X-ray crystallography

artículo científico publicado en 2013

PARP1 ADP-ribosylates lysine residues of the core histone tails

artículo científico publicado en 2010

Pathways and intermediates of amyloid fibril formation

artículo científico publicado en 2007

Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis

artículo científico publicado en 2008

Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges

artículo científico publicado en 2015

Peptide binding to the PDZ3 domain by conformational selection

artículo científico publicado en 2012

Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylketonuria

artículo científico publicado en 2012

Phi-value analysis by molecular dynamics simulations of reversible folding

artículo científico publicado en 2005

Photocontrol of reversible amyloid formation with a minimal-design peptide

artículo científico publicado en 2012

Protein Structural Memory Influences Ligand Binding Mode(s) and Unbinding Rates

artículo científico publicado en 2016

Protein structure-based drug design: from docking to molecular dynamics

artículo científico publicado en 2017

Proteomic analyses identify ARH3 as a serine mono-ADP-ribosylhydrolase

artículo científico publicado en 2017

Pyrrolo[3,2-b]quinoxaline derivatives as types I1/2 and II Eph tyrosine kinase inhibitors: structure-based design, synthesis, and in vivo validation

artículo científico publicado en 2014

Quantum mechanical methods for drug design

scientific article published on January 2010

Reducing the Flexibility of Type II Dehydroquinase for Inhibition: A Fragment-Based Approach and Molecular Dynamics Study.

artículo científico publicado en 2017

SAPPHIRE-based clustering

scientific article published on 09 September 2020

Selectively Disrupting m6A-Dependent Protein-RNA Interactions with Fragments

artículo científico publicado en 2020

Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane

artículo científico publicado en 2006

Ser170 controls the conformational multiplicity of the loop 166-175 in prion proteins: implication for conversion and species barrier.

artículo científico publicado en 2007

Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates

scientific article published on 11 April 2019

Small molecule binding to proteins: affinity and binding/unbinding dynamics from atomistic simulations

artículo científico publicado en 2011

Small-Molecule Inhibitors of METTL3, the Major Human Epitranscriptomic Writer

artículo científico publicado en 2020

Specific Inhibition of β-Secretase Processing of the Alzheimer Disease Amyloid Precursor Protein

artículo científico publicado en 2016

Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure

artículo científico publicado en 2014

Structural Analysis of Small-Molecule Binding to the BAZ2A and BAZ2B Bromodomains

scientific article published on 21 June 2018

Structural Analysis of the Binding of Type I, I1/2, and II Inhibitors to Eph Tyrosine Kinases

artículo científico publicado en 2014

Structural and Dynamic Insights into Redundant Function of YTHDF Proteins

scientific article published on 19 October 2020

Structural basis for inhibiting β-amyloid oligomerization by a non-coded β-breaker-substituted endomorphin analogue

artículo científico publicado en 2011

Structure-based discovery of selective BRPF1 bromodomain inhibitors

artículo científico publicado en 2018

Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4).

artículo científico publicado en 2009

Structure-based tailoring of compound libraries for high-throughput screening: discovery of novel EphB4 kinase inhibitors

artículo científico publicado en 2008

Structured water molecules in the binding site of bromodomains can be displaced by cosolvent

artículo científico publicado en 2013

Surfactant effects on amyloid aggregation kinetics

scientific article published on 14 October 2011

Synthesis, radiolabelling and initial biological characterisation of 18F-labelled xanthine derivatives for PET imaging of Eph receptors

scientific article published on 07 April 2020

The "Gatekeeper" Residue Influences the Mode of Binding of Acetyl Indoles to Bromodomains

artículo científico publicado en 2016

The 3A6-TCR/superagonist/HLA-DR2a complex shows similar interface and reduced flexibility compared to the complex with self-peptide

artículo científico publicado en 2019

The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes

artículo científico publicado en 2017

The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes.

artículo científico publicado en 2017

The Free Energy Landscape of Small Molecule Unbinding ⬇️

artículo científico publicado el 3 de febrero de 2011

The protein folding network

scientific article published on 01 September 2004

The protonation state of the catalytic aspartates in plasmepsin II

artículo científico publicado en 2007

The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour.

artículo científico publicado en 2010

Three stories on Eph kinase inhibitors: From in silico discovery to in vivo validation

artículo científico publicado en 2016

Twenty Crystal Structures of Bromodomain and PHD Finger Containing Protein 1 (BRPF1)/Ligand Complexes Reveal Conserved Binding Motifs and Rare Interactions

artículo científico publicado en 2016

Unfolding transition state and intermediates of the tumor suppressor p16INK4a investigated by molecular dynamics simulations.

artículo científico publicado en 2006

Virtual screen to NMR (VS2NMR): Discovery of fragment hits for the CBP bromodomain.

artículo científico publicado en 2017

Weak temperature dependence of the free energy surface and folding pathways of structured peptides

artículo científico publicado en 2002

Weighted Distance Functions Improve Analysis of High-Dimensional Data: Application to Molecular Dynamics Simulations

artículo científico publicado en 2015

Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: a simulation study

artículo científico publicado en 2013

Wordom: a program for efficient analysis of molecular dynamics simulations

artículo científico publicado en 2007

Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces

artículo científico publicado en 2010

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