List of works - Amedeo Caflisch

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

scientific article published in March 2010

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

scientific article

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

scientific article published on April 2009

A Reader-Based Assay for m6A Writers and Erasers

scientific article published on 04 February 2019

A Small-Molecule Inhibitor of Lin28.

scientific article

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

scientific article published on 24 March 2015

A double-headed cathepsin B inhibitor devoid of warhead

scientific article

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

scientific article

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

scientific article

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

scientific article (publication date: May 2009)

Alpha-Helix folding in the presence of structural constraints.

scholarly article

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

scientific article published on 24 December 2008

Amyloid fibril polymorphism is under kinetic control

scientific article published on 01 October 2010

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

scientific article published on 4 September 2017

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

scientific article published on 08 September 2020

Assessment of the fragment docking program SEED

scientific article published on 21 August 2020

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

scientific article published on 21 January 2021

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

scientific article published in February 2004

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

scientific article

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

scientific article published on June 2015

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

scientific article published in April 2009

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

scientific article published in January 2002

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

scientific article published on 25 February 2013

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

scientific article published on 21 September 2007

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

scientific article published on 7 February 2018

Complementing ultrafast shape recognition with an optical isomerism descriptor ⬇️

scientific article published on September 29, 2010

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

scientific article

Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition

scientific article

Current kinase inhibitors cover a tiny fraction of fragment space.

scientific article published on 10 April 2015

Data management system for distributed virtual screening

scientific article

Data publication with the structural biology data grid supports live analysis

scientific article

Delineation of folding pathways of a β-sheet miniprotein

scientific article published on 17 October 2011

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

scientific article

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

scientific article

Discovery of BAZ2A Bromodomain Ligands

Discovery of BAZ2A bromodomain ligands.

scientific article published on 12 August 2017

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

scientific article

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

scientific article

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

scientific article published in September 2017

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

scientific article published on 11 August 2013

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

scientific article (publication date: 2009)

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

scientific article

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

scientific article

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

scientific article published on 10 February 2014

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

scientific article

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

scientific article (publication date: August 2009)

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

scientific article

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

scientific article published on 17 July 2018

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

scientific article published on 3 October 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

scientific article published on 27 December 2018

Does bromodomain flexibility influence histone recognition?

scientific article published on 25 May 2013

Dynamic microfluidic control of supramolecular peptide self-assembly

scientific article

Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories

scientific article published on 10 February 2012

Efficient evaluation of binding free energy using continuum electrostatics solvation

scientific article

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

scientific article published on November 30, 2003

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

scientific article published on 17 April 2008

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

scientific article published on 01 January 2007

Estimation of protein folding probability from equilibrium simulations

scientific article published on 01 May 2005

Evaluation of a fast implicit solvent model for molecular dynamics simulations

scientific article (publication date: 2002)

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

scientific article

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

scientific article published on 01 May 2010

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

scientific article published in August 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.

scientific article published in November 2017

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

scientific article

Fragment-based de novo ligand design by multiobjective evolutionary optimization

scientific article

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

scientific article

Fragment-based in silico screening of bromodomain ligands

scientific article

Free Energy Guided Sampling

scientific article published on 04 May 2012

Free Energy Guided Sampling

scientific article published on 13 August 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

scientific article

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

scientific article

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

scientific article

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?

scientific article published on 24 April 2012

How does a simplified-sequence protein fold?

scientific article published on September 2009

In Silico Identification of JMJD3 Demethylase Inhibitors

scientific article published on 03 October 2018

In silico discovery of beta-secretase inhibitors.

scientific article published in April 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

scientific article

Interpreting the aggregation kinetics of amyloid peptides

scientific article published on 05 June 2006

Is quantum mechanics necessary for predicting binding free energy?

scientific article published on 25 June 2008

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

scientific article published on 26 November 2009

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

scientific article published on 06 January 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

scientific article published on 01 March 2008

Kinetic response of a photoperturbed allosteric protein

scientific article

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.

scientific article published on 10 March 2013

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

scientific article

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

scientific article published on 31 January 2013

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

scientific article published on 13 August 2010

Molecular dynamics in drug design.

scientific article

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

scientific article published on 20 August 2008

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

scientific article published on 08 February 2017

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

scientific article published on 3 July 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

scientific article published on 15 May 2013

On the orientation of the catalytic dyad in aspartic proteases

scientific article published in May 2010

On the removal of initial state bias from simulation data

scientific article published on 01 March 2019

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

scientific article published on July 2008

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

scientific article

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

scientific article

PARP1 ADP-ribosylates lysine residues of the core histone tails

scientific article

Pathways and intermediates of amyloid fibril formation

scientific article published on 04 October 2007

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

scientific article published in December 2008

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

scientific article published on May 2015

Peptide binding to the PDZ3 domain by conformational selection

scientific article published on 28 July 2012

Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylketonuria

scientific article

Phi-value analysis by molecular dynamics simulations of reversible folding

scientific article

Photocontrol of reversible amyloid formation with a minimal-design peptide

scientific article published on 16 July 2012

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

scientific article published on 22 January 2016

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

scientific article published on 14 November 2017

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

scientific article published on 12 December 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

scientific article

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.

scientific article published on 9 August 2017

SAPPHIRE-based clustering

scientific article published on 09 September 2020

Selectively Disrupting m6A-Dependent Protein-RNA Interactions with Fragments

scientific article published on 02 March 2020

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

scientific article

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

scientific article published on 23 May 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

scientific article published on 14 June 2011

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

scientific article published on 11 March 2020

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 19 September 2011

Structure-based discovery of selective BRPF1 bromodomain inhibitors

scientific article published on 02 June 2018

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

scientific article published in October 2009

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

scientific article

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

scientific article published on 26 June 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

scientific article

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

scientific article published on 25 June 2019

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

scientific article published in November 2017

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

scientific article published on 10 August 2017

The free energy landscape of small molecule unbinding

scientific article (publication date: February 2011)

The protein folding network

scientific article published on 01 September 2004

The protonation state of the catalytic aspartates in plasmepsin II

scientific article published on 25 July 2007

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

scientific article published on 21 January 2010

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

scientific article published on 2 February 2016

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 01 May 2002

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

scientific article

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

scientific article published on 18 October 2013

Wordom: a program for efficient analysis of molecular dynamics simulations.

scientific article published on 23 August 2007

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

scientific article

List of works by Amedeo Caflisch

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

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

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

A Reader-Based Assay for m6A Writers and Erasers

A Small-Molecule Inhibitor of Lin28.

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

A double-headed cathepsin B inhibitor devoid of warhead

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

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

A sphere-based model for the electrostatics of globular proteins

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

Alpha-Helix folding in the presence of structural constraints.

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

Amyloid fibril polymorphism is under kinetic control

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

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

Assessment of the fragment docking program SEED

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

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

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

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

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

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

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

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

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

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

Complementing ultrafast shape recognition with an optical isomerism descriptor ⬇️

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

Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition

Current kinase inhibitors cover a tiny fraction of fragment space.

Data management system for distributed virtual screening

Data publication with the structural biology data grid supports live analysis

Delineation of folding pathways of a β-sheet miniprotein

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

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

Discovery of BAZ2A Bromodomain Ligands

Discovery of BAZ2A bromodomain ligands.

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

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

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

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

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

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

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

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

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

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

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

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

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

Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric

Disulfide bridge formation influences ligand recognition by the ATAD2 bromodomain

Does bromodomain flexibility influence histone recognition?

Dynamic microfluidic control of supramolecular peptide self-assembly

Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories

Efficient evaluation of binding free energy using continuum electrostatics solvation

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

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

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

Estimation of protein folding probability from equilibrium simulations

Evaluation of a fast implicit solvent model for molecular dynamics simulations

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

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

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

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

Focused conformational sampling in proteins.

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

Fragment-based de novo ligand design by multiobjective evolutionary optimization

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

Fragment-based in silico screening of bromodomain ligands

Free Energy Guided Sampling

Free Energy Guided Sampling

Free Energy Surfaces from Single-Distance Information

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

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

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

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

How Does Darunavir Prevent HIV-1 Protease Dimerization?