List of works - Chun Wu

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

scientific article (publication date: December 2003)

Accurate ab Initio Study on the Hydrogen-Bond Pairs in Protein Secondary Structures

scientific article published on January 2007

An Experimental and Molecular Dynamics Study of Red Fluorescent Protein mCherry in Novel Aqueous Amino Acid Ionic Liquids.

scientific article

Analysis of the Amyloidogenic Potential of Pufferfish (Takifugu rubripes) Islet Amyloid Polypeptide Highlights the Limitations of Thioflavin-T Assays and the Difficulties in Defining Amyloidogenicity

scientific article

Assessing the Performance of Popular Quantum Mechanics and Molecular Mechanics Methods and Revealing the Sequence-Dependent Energetic Features Using 100 Tetrapeptide Models

scientific article published on 13 April 2010

Aβ(39-42) modulates Aβ oligomerization but not fibril formation

scientific article published on 23 December 2011

Binding Interactions of Ergotamine and Dihydroergotamine to 5-Hydroxytryptamine Receptor 1B (5-HT1b) Using Molecular Dynamics Simulations and Dynamic Network Analysis

scientific article published on 02 March 2020

Binding modes and pathway of RHPS4 to human telomeric G-quadruplex and duplex DNA probed by all-atom molecular dynamics simulations with explicit solvent

scientific article

Binding modes of thioflavin-T to the single-layer beta-sheet of the peptide self-assembly mimics

scientific article published on 30 September 2009

Binding of BRACO19 to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent

scientific article published on 13 March 2019

Binding of Congo red to amyloid protofibrils of the Alzheimer Aβ(9-40) peptide probed by molecular dynamics simulations.

scientific article

Binding of Telomestatin to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent.

scientific article published on 15 September 2016

Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands

scientific article published on 8 August 2017

Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide

scientific article

Coarse-grained models for protein aggregation.

scientific article published on March 2011

Computational Study of Anticancer Drug Resistance Caused by 10 Topisomerase I Mutations, Including 7 Camptothecin Analogs and Lucanthone.

scientific article published on September 2016

Computational analysis of Amsacrine resistance in human topoisomerase II alpha mutants (R487K and E571K) using homology modeling, docking and all-atom molecular dynamics simulation in explicit solvent

scientific article published on 4 January 2017

Computational and experimental analyses reveal the essential roles of interdomain linkers in the biological function of chemotaxis histidine kinase CheA.

scientific article published on 21 September 2012

Convergence of replica exchange molecular dynamics

scientific article published in October 2005

Defining the molecular basis of amyloid inhibitors: human islet amyloid polypeptide-insulin interactions

scientific article

Derivative matrix isopotential synchronous fluorescence spectroscopy for the direct determination of 1-hydroxypyrene as a urinary biomarker of exposure to polycyclic aromatic hydrocarbons

scientific article

Development of a novel series of non-natural triaryl agonists and antagonists of the Pseudomonas aeruginosa LasR quorum sensing receptor.

scientific article published on 20 October 2016

Dual binding modes of Congo red to amyloid protofibril surface observed in molecular dynamics simulations

scientific article

Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations

scientific article published on October 2009

Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations ⬇️

scientific article published on June 13, 2012

Elongation of ordered peptide aggregate of an amyloidogenic hexapeptide NFGAIL observed in molecular dynamics simulations with explicit solvent

scientific article

Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations

scholarly article

Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

scientific article published on June 2008

GDP Release from the Open Conformation of Gα Requires Allosteric Signaling from the Agonist-Bound Human β2 Adrenergic Receptor

scientific article published on 11 August 2020

Hetero-oligomeric Amyloid Assembly and Mechanism: Prion Fragment PrP(106-126) Catalyzes the Islet Amyloid Polypeptide β-Hairpin

scientific article published on 23 July 2018

Ion mobility spectrometry reveals the mechanism of amyloid formation of Aβ(25-35) and its modulation by inhibitors at the molecular level: epigallocatechin gallate and scyllo-inositol

scientific article

Mechanism of C-Terminal Fragments of Amyloid β-Protein as Aβ Inhibitors: Do C-Terminal Interactions Play a Key Role in Their Inhibitory Activity?

scientific article published on 6 October 2015

Molecular Dynamics Simulations and Free Energy Analyses on the Dimer Formation of an Amyloidogenic Heptapeptide from Human β2-Microglobulin: Implication for the Protofibril Structure

article

Molecular dynamics simulation of biased agonists at the dopamine D2 receptor suggests the mechanism of receptor functional selectivity

scientific article published on 13 November 2018

Molecular structures of quiescently grown and brain-derived polymorphic fibrils of the Alzheimer amyloid abeta9-40 peptide: a comparison to agitated fibrils

scientific article

Oligomers of the prion protein fragment 106-126 are likely assembled from beta-hairpins in solution, and methionine oxidation inhibits assembly without altering the peptide's monomeric conformation

scientific article published in January 2010

On the origin of the stronger binding of PIB over thioflavin T to protofibrils of the Alzheimer amyloid-β peptide: a molecular dynamics study.

scientific article

On the origins of the weak folding cooperativity of a designed ββα ultrafast protein FSD-1.

scientific article

Phenol red interacts with the protofibril-like oligomers of an amyloidogenic hexapeptide NFGAIL through both hydrophobic and aromatic contacts.

scientific article

Probing the Binding Pathway of BRACO19 to a Parallel-Stranded Human Telomeric G-Quadruplex Using Molecular Dynamics Binding Simulation with AMBER DNA OL15 and Ligand GAFF2 Force Fields.

scientific article published on 13 October 2017

Rapid simultaneous determination of four anthracene derivatives using a single non-linear variable-angle synchronous fluorescence spectrum

scientific article published in December 2000

Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides

scientific article

Structural similarities and differences between amyloidogenic and non-amyloidogenic islet amyloid polypeptide (IAPP) sequences and implications for the dual physiological and pathological activities of these peptides

scientific article

Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces.

scientific article published on 28 March 2016

The amyloid formation mechanism in human IAPP: dimers have β-strand monomer-monomer interfaces

scientific article

The binding of thioflavin T and its neutral analog BTA-1 to protofibrils of the Alzheimer's disease Abeta(16-22) peptide probed by molecular dynamics simulations

scientific article published on 07 October 2008

The linker between the dimerization and catalytic domains of the CheA histidine kinase propagates changes in structure and dynamics that are important for enzymatic activity

scientific article published on 28 January 2014

Three-Dimensional Structure of RNA Monomeric G-Quadruplex Containing ALS and FTD Related G4C2 Repeat and Its Binding with TMPyP4 Probed by Homology Modeling based on Experimental Constraints and Molecular Dynamics Simulations

scientific article published on 19 December 2019

To Probe Full and Partial Activation of Human Peroxisome Proliferator-Activated Receptors by Pan-Agonist Chiglitazar Using Molecular Dynamics Simulations

scientific article published on 01 April 2020

To probe interaction of morphine and IBNtxA with 7TM and 6TM variants of the human μ-opioid receptor using all-atom molecular dynamics simulations with an explicit membrane

scientific article published on 21 December 2017

To probe the binding pathway of a selective compound (D089-0563) to c-MYC Pu24 G-quadruplex using free ligand binding simulations and Markov state model analysis

scientific article published on 01 October 2020

List of works by Chun Wu

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

Accurate ab Initio Study on the Hydrogen-Bond Pairs in Protein Secondary Structures

An Experimental and Molecular Dynamics Study of Red Fluorescent Protein mCherry in Novel Aqueous Amino Acid Ionic Liquids.

Analysis of the Amyloidogenic Potential of Pufferfish (Takifugu rubripes) Islet Amyloid Polypeptide Highlights the Limitations of Thioflavin-T Assays and the Difficulties in Defining Amyloidogenicity

Assessing the Performance of Popular Quantum Mechanics and Molecular Mechanics Methods and Revealing the Sequence-Dependent Energetic Features Using 100 Tetrapeptide Models

Aβ(39-42) modulates Aβ oligomerization but not fibril formation

Binding Interactions of Ergotamine and Dihydroergotamine to 5-Hydroxytryptamine Receptor 1B (5-HT1b) Using Molecular Dynamics Simulations and Dynamic Network Analysis

Binding modes and pathway of RHPS4 to human telomeric G-quadruplex and duplex DNA probed by all-atom molecular dynamics simulations with explicit solvent

Binding modes of thioflavin-T to the single-layer beta-sheet of the peptide self-assembly mimics

Binding of BRACO19 to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent

Binding of Congo red to amyloid protofibrils of the Alzheimer Aβ(9-40) peptide probed by molecular dynamics simulations.

Binding of Telomestatin to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent.

Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands

Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide

Coarse-grained models for protein aggregation.

Computational Study of Anticancer Drug Resistance Caused by 10 Topisomerase I Mutations, Including 7 Camptothecin Analogs and Lucanthone.

Computational analysis of Amsacrine resistance in human topoisomerase II alpha mutants (R487K and E571K) using homology modeling, docking and all-atom molecular dynamics simulation in explicit solvent

Computational and experimental analyses reveal the essential roles of interdomain linkers in the biological function of chemotaxis histidine kinase CheA.

Convergence of replica exchange molecular dynamics

Defining the molecular basis of amyloid inhibitors: human islet amyloid polypeptide-insulin interactions

Derivative matrix isopotential synchronous fluorescence spectroscopy for the direct determination of 1-hydroxypyrene as a urinary biomarker of exposure to polycyclic aromatic hydrocarbons

Development of a novel series of non-natural triaryl agonists and antagonists of the Pseudomonas aeruginosa LasR quorum sensing receptor.

Dual binding modes of Congo red to amyloid protofibril surface observed in molecular dynamics simulations

Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations

Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations ⬇️

Elongation of ordered peptide aggregate of an amyloidogenic hexapeptide NFGAIL observed in molecular dynamics simulations with explicit solvent

Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations

Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

GDP Release from the Open Conformation of Gα Requires Allosteric Signaling from the Agonist-Bound Human β2 Adrenergic Receptor

Hetero-oligomeric Amyloid Assembly and Mechanism: Prion Fragment PrP(106-126) Catalyzes the Islet Amyloid Polypeptide β-Hairpin

Ion mobility spectrometry reveals the mechanism of amyloid formation of Aβ(25-35) and its modulation by inhibitors at the molecular level: epigallocatechin gallate and scyllo-inositol

Mechanism of C-Terminal Fragments of Amyloid β-Protein as Aβ Inhibitors: Do C-Terminal Interactions Play a Key Role in Their Inhibitory Activity?

Molecular Dynamics Simulations and Free Energy Analyses on the Dimer Formation of an Amyloidogenic Heptapeptide from Human β2-Microglobulin: Implication for the Protofibril Structure

Molecular dynamics simulation of biased agonists at the dopamine D2 receptor suggests the mechanism of receptor functional selectivity

Molecular structures of quiescently grown and brain-derived polymorphic fibrils of the Alzheimer amyloid abeta9-40 peptide: a comparison to agitated fibrils

Oligomers of the prion protein fragment 106-126 are likely assembled from beta-hairpins in solution, and methionine oxidation inhibits assembly without altering the peptide's monomeric conformation

On the origin of the stronger binding of PIB over thioflavin T to protofibrils of the Alzheimer amyloid-β peptide: a molecular dynamics study.

On the origins of the weak folding cooperativity of a designed ββα ultrafast protein FSD-1.

Phenol red interacts with the protofibril-like oligomers of an amyloidogenic hexapeptide NFGAIL through both hydrophobic and aromatic contacts.

Probing the Binding Pathway of BRACO19 to a Parallel-Stranded Human Telomeric G-Quadruplex Using Molecular Dynamics Binding Simulation with AMBER DNA OL15 and Ligand GAFF2 Force Fields.

Rapid simultaneous determination of four anthracene derivatives using a single non-linear variable-angle synchronous fluorescence spectrum

Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides

Structural similarities and differences between amyloidogenic and non-amyloidogenic islet amyloid polypeptide (IAPP) sequences and implications for the dual physiological and pathological activities of these peptides

Surface force measurements and simulations of mussel-derived peptide adhesives on wet organic surfaces.

The amyloid formation mechanism in human IAPP: dimers have β-strand monomer-monomer interfaces

The binding of thioflavin T and its neutral analog BTA-1 to protofibrils of the Alzheimer's disease Abeta(16-22) peptide probed by molecular dynamics simulations

The linker between the dimerization and catalytic domains of the CheA histidine kinase propagates changes in structure and dynamics that are important for enzymatic activity

Three-Dimensional Structure of RNA Monomeric G-Quadruplex Containing ALS and FTD Related G4C2 Repeat and Its Binding with TMPyP4 Probed by Homology Modeling based on Experimental Constraints and Molecular Dynamics Simulations

To Probe Full and Partial Activation of Human Peroxisome Proliferator-Activated Receptors by Pan-Agonist Chiglitazar Using Molecular Dynamics Simulations

To probe interaction of morphine and IBNtxA with 7TM and 6TM variants of the human μ-opioid receptor using all-atom molecular dynamics simulations with an explicit membrane

To probe the binding pathway of a selective compound (D089-0563) to c-MYC Pu24 G-quadruplex using free ligand binding simulations and Markov state model analysis