List of works - Feng Ding

A Framework of Paracellular Transport via Nanoparticles-Induced Endothelial Leakiness

scientific article published on 08 September 2021

A Thermodynamics Model for the Emergence of a Stripe-like Binary SAM on a Nanoparticle Surface.

scientific article published on 20 July 2015

A hidden aggregation-prone structure in the heart of hypoxia inducible factor prolyl hydroxylase

scientific article published on 12 February 2016

A structural model reveals energy transduction in dynein

scholarly article

Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms

scientific article published on 2 May 2008

Ab initio folding of proteins with all-atom discrete molecular dynamics

scientific article published on July 2008

Active nuclear receptors exhibit highly correlated AF-2 domain motions

scientific article

Amphiphilic surface chemistry of fullerenols is necessary for inhibiting the amyloid aggregation of alpha-synuclein NACore

scientific article published on 01 June 2019

Amyloid Aggregation under the Lens of Liquid-Liquid Phase Separation

scientific article published on 24 December 2020

Amyloid Self-Assembly of hIAPP8-20 via the Accumulation of Helical Oligomers, α-Helix to β-Sheet Transition, and Formation of β-Barrel Intermediates

scientific article published on 25 March 2019

Automated minimization of steric clashes in protein structures

scientific article

Binding of cytoskeletal proteins with silver nanoparticles

scholarly article in RSC Advances, vol. 3 no. 44, 2013

Cofibrillization of Pathogenic and Functional Amyloid Proteins with Gold Nanoparticles against Amyloidogenesis.

scientific article published on 2 November 2017

Competitive binding of natural amphiphiles with graphene derivatives

scientific article published on January 2013

Computational Evaluation of Protein Stability Change upon Mutations ⬇️

scientific article published on January 1, 2010

Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models

scientific article published on 25 August 2022

Computational approaches to understanding protein aggregation in neurodegeneration

scientific article published on 11 March 2014

Contrasting effects of nanoparticle-protein attraction on amyloid aggregation

scientific article

Deviation from the Unimolecular Micelle Paradigm of PAMAM Dendrimers Induced by Strong Interligand Interactions

Direct Observation of Protein Folding, Aggregation, and a Prion-like Conformational Conversion

scientific article published in Journal of Biological Chemistry

Direct molecular dynamics observation of protein folding transition state ensemble

scientific article

Direct observation of a single nanoparticle-ubiquitin corona formation

scientific article

Discrete molecular dynamics

article

Discrete molecular dynamics simulations of peptide aggregation

scientific article published on 29 April 2004

Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization

scientific article

Distinct oligomerization and fibrillization dynamics of amyloid core sequences of amyloid-beta and islet amyloid polypeptide

scientific article published on 17 October 2017

Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation

scholarly article

Effect of fullerenol surface chemistry on nanoparticle binding-induced protein misfolding.

scientific article

Effects of Protein Corona on IAPP Amyloid Aggregation, Fibril Remodelling, and Cytotoxicity

scientific article

Elevated amyloidoses of human IAPP and amyloid beta by lipopolysaccharide and their mitigation by carbon quantum dots

scientific article published on 03 June 2020

Emergence of protein fold families through rational design

scientific article

Engineered allosteric activation of kinases in living cells

scientific article

Eris: an automated estimator of protein stability

scientific article published in June 2007

Fast complementation of split fluorescent protein triggered by DNA hybridization

scholarly article

Fidelity of the protein structure reconstruction from inter-residue proximity constraints.

scientific article

Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model

scientific article

Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis

scientific article published in November 2003

G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase

scientific article

Gaia: automated quality assessment of protein structure models

scientific article

Graphene oxide inhibits hIAPP amyloid fibrillation and toxicity in insulin-producing NIT-1 cells

scientific article published on 2 December 2015

Graphene quantum dots against human IAPP aggregation and toxicity in vivo

article

Harnessing a physiologic mechanism for siRNA delivery with mimetic lipoprotein particles

scientific article published on 5 June 2012

Human Plasma Protein Corona of Aβ Amyloid and Its Impact on Islet Amyloid Polypeptide Cross-Seeding

scientific article published on 21 January 2020

Hybrid dynamics simulation engine for metalloproteins

scientific article

Identifying importance of amino acids for protein folding from crystal structures

scientific article published in January 2003

Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95

scientific article published in Nature Communications

Implications of peptide assemblies in amyloid diseases

scientific article

Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark

scientific article

Inhibition of IAPP aggregation by insulin depends on the insulin oligomeric state regulated by zinc ion concentration.

scientific article published on 4 February 2015

Inhibition of amyloid beta toxicity in zebrafish with a chaperone-gold nanoparticle dual strategy

scientific article published on 22 August 2019

Inhibition of hIAPP Amyloid Aggregation and Pancreatic β-Cell Toxicity by OH-Terminated PAMAM Dendrimer.

scientific article published on 25 January 2016

Interaction of firefly luciferase and silver nanoparticles and its impact on enzyme activity ⬇️

scientific article published on July 30, 2013

Islet Amyloid Polypeptide Promotes Amyloid-beta Aggregation by Binding-induced Helix-unfolding of the Amyloidogenic Core

scientific article published on 29 January 2018

Labeling native bacterial RNA in live cells

scientific article published on 15 April 2014

Local unfolding of Cu, Zn superoxide dismutase monomer determines the morphology of fibrillar aggregates

scientific article published on 21 December 2011

Lysophosphatidylcholine modulates the aggregation of human islet amyloid polypeptide

scientific article published on 8 November 2017

Mechanism for the alpha-helix to beta-hairpin transition

scientific article

Mechanistic Insights from Discrete Molecular Dynamics Simulations of Pesticide-Nanoparticle Interactions.

scientific article published on 7 July 2017

Mitigating Human IAPP Amyloidogenesis In Vivo with Chiral Silica Nanoribbons

scientific article published on 07 October 2018

Modeling backbone flexibility improves protein stability estimation.

scientific article

Modulating protein amyloid aggregation with nanomaterials.

scientific article published on 28 July 2017

Molecular dynamics simulation of amyloid beta dimer formation

scientific article published on October 2004

Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism

scientific article

Molecular origin of polyglutamine aggregation in neurodegenerative diseases

scientific article

Multiple folding pathways of the SH3 domain

scientific article

Multiscale modeling of nucleosome dynamics

scientific article published on December 2006

N-terminal strands of filamin Ig domains act as a conformational switch under biological forces

scientific article

NanoEHS beyond Toxicity - Focusing on Biocorona

scientific article published in June 2017

Nanoscale inhibition of polymorphic and ambidextrous IAPP amyloid aggregation with small molecules

scientific article published on 01 July 2018

Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics

scientific article published in February 2009

New Insights into FAK Signaling and Localization Based on Detection of a FAT Domain Folding Intermediate

New models of Tetrahymena telomerase RNA from experimentally derived constraints and modeling

scientific article published on 3 December 2012

Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-like β-Sandwich Proteins

scientific article

Novel application of a perturbed photonic crystal: High-quality filter

Nucleation of β-rich oligomers and β-barrels in the early aggregation of human islet amyloid polypeptide

scientific article published on 28 November 2018

On the significance of an RNA tertiary structure prediction

scientific article

PAMAM dendrimers and graphene: materials for removing aromatic contaminants from water

scientific article

Parallel folding pathways in the SH3 domain protein

scientific article

Physical and Toxicological Profiles of Human IAPP Amyloids and Plaques

scientific article published on 22 November 2018

Polyglutamine induced misfolding of huntingtin exon1 is modulated by the flanking sequences

scientific article

Predicting binding affinity of CSAR ligands using both structure-based and ligand-based approaches

scientific article

Probing the modulated formation of gold nanoparticles-beta-lactoglobulin corona complexes and their applications

scientific article published on 4 September 2017

Profiling the Serum Protein Corona of Fibrillar Human Islet Amyloid Polypeptide

Promotion or Inhibition of Islet Amyloid Polypeptide Aggregation by Zinc Coordination Depends on Its Relative Concentration

scientific article published on 25 November 2015

Protein folding: then and now

scientific article

RNA tertiary structure analysis by 2'-hydroxyl molecular interference

scientific article

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

scientific article published on 16 April 2015

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

scientific article published on 05 May 2020

RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction

scientific article published on 23 February 2012

Rapid flexible docking using a stochastic rotamer library of ligands

scientific article

Rational design of a ligand-controlled protein conformational switch

scientific article published on 8 April 2013

Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations

scientific article

Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain

scientific article published on June 2010

Scaling behavior and structure of denatured proteins

scientific article published in July 2005

Simple but predictive protein models

article

Single-Molecular Heteroamyloidosis of Human Islet Amyloid Polypeptide

scientific article published on 29 August 2019

Stabilizing Off-pathway Oligomers by Polyphenol Nanoassemblies for IAPP Aggregation Inhibition

scientific article

Star Polymers Reduce Islet Amyloid Polypeptide Toxicity via Accelerated Amyloid Aggregation.

scientific article published on 16 October 2017

Statistical analysis of SHAPE-directed RNA secondary structure modeling

scientific article published on 14 January 2013

Structural and Thermodynamic Effects of Post-translational Modifications in Mutant and Wild Type Cu, Zn Superoxide Dismutase ⬇️

scientific article published on March 23, 2011

Structural and dynamic determinants of protein-peptide recognition

scientific article

Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity

scientific article

Structural basis for μ-opioid receptor binding and activation

scientific article

Structure-function relationship of PAMAM dendrimers as robust oil dispersants

scientific article published on 15 October 2014

Structures and dynamics of β-barrel oligomer intermediates of amyloid-beta16-22 aggregation

scientific article published on 14 March 2018

Submillisecond elastic recoil reveals molecular origins of fibrin fiber mechanics

scientific article published on June 2013

Synthesis and in vitro properties of iron oxide nanoparticles grafted with brushed phosphorylcholine and polyethylene glycol

The Length Dependence of the PolyQ-mediated Protein Aggregation

scientific article published in Journal of Biological Chemistry

Thermostability and reversibility of silver nanoparticle–protein binding

scientific article published on 02 December 2014

Three-dimensional RNA structure refinement by hydroxyl radical probing

scientific article

Topological Determinants of Protein Domain Swapping

article published in 2006

Topological determinants of protein folding

scientific article

Understanding Effects of PAMAM Dendrimer Size and Surface Chemistry on Serum Protein Binding with Discrete Molecular Dynamics Simulations

scientific article published on 31 July 2018

iFold: a platform for interactive folding simulations of proteins

scientific article published in 2006

iFoldRNA: three-dimensional RNA structure prediction and folding

scientific article

αB-Crystallin Chaperone Inhibits Aβ Aggregation by Capping the β-Sheet-Rich Oligomers and Fibrils

scientific article published on 29 October 2020

β-barrel Oligomers as Common Intermediates of Peptides Self-Assembling into Cross-β Aggregates.

scientific article published on 9 July 2018

List of works by Feng Ding

A Framework of Paracellular Transport via Nanoparticles-Induced Endothelial Leakiness

A Thermodynamics Model for the Emergence of a Stripe-like Binary SAM on a Nanoparticle Surface.

A hidden aggregation-prone structure in the heart of hypoxia inducible factor prolyl hydroxylase

A structural model reveals energy transduction in dynein

Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms

Ab initio folding of proteins with all-atom discrete molecular dynamics

Active nuclear receptors exhibit highly correlated AF-2 domain motions

Amphiphilic surface chemistry of fullerenols is necessary for inhibiting the amyloid aggregation of alpha-synuclein NACore

Amyloid Aggregation under the Lens of Liquid-Liquid Phase Separation

Amyloid Self-Assembly of hIAPP8-20 via the Accumulation of Helical Oligomers, α-Helix to β-Sheet Transition, and Formation of β-Barrel Intermediates

Automated minimization of steric clashes in protein structures

Binding of cytoskeletal proteins with silver nanoparticles

Cofibrillization of Pathogenic and Functional Amyloid Proteins with Gold Nanoparticles against Amyloidogenesis.

Competitive binding of natural amphiphiles with graphene derivatives

Computational Evaluation of Protein Stability Change upon Mutations ⬇️

Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models

Computational approaches to understanding protein aggregation in neurodegeneration

Contrasting effects of nanoparticle-protein attraction on amyloid aggregation

Deviation from the Unimolecular Micelle Paradigm of PAMAM Dendrimers Induced by Strong Interligand Interactions

Direct Observation of Protein Folding, Aggregation, and a Prion-like Conformational Conversion

Direct molecular dynamics observation of protein folding transition state ensemble

Direct observation of a single nanoparticle-ubiquitin corona formation

Discrete molecular dynamics

Discrete molecular dynamics simulations of peptide aggregation

Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization

Distinct oligomerization and fibrillization dynamics of amyloid core sequences of amyloid-beta and islet amyloid polypeptide

Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation

Effect of fullerenol surface chemistry on nanoparticle binding-induced protein misfolding.

Effects of Protein Corona on IAPP Amyloid Aggregation, Fibril Remodelling, and Cytotoxicity

Elevated amyloidoses of human IAPP and amyloid beta by lipopolysaccharide and their mitigation by carbon quantum dots

Emergence of protein fold families through rational design

Engineered allosteric activation of kinases in living cells

Eris: an automated estimator of protein stability

Fast complementation of split fluorescent protein triggered by DNA hybridization

Fidelity of the protein structure reconstruction from inter-residue proximity constraints.

Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model

Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis

G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase

Gaia: automated quality assessment of protein structure models

Graphene oxide inhibits hIAPP amyloid fibrillation and toxicity in insulin-producing NIT-1 cells

Graphene quantum dots against human IAPP aggregation and toxicity in vivo

Harnessing a physiologic mechanism for siRNA delivery with mimetic lipoprotein particles

Human Plasma Protein Corona of Aβ Amyloid and Its Impact on Islet Amyloid Polypeptide Cross-Seeding

Hybrid dynamics simulation engine for metalloproteins

Identifying importance of amino acids for protein folding from crystal structures

Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95

Implications of peptide assemblies in amyloid diseases

Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark

Inhibition of IAPP aggregation by insulin depends on the insulin oligomeric state regulated by zinc ion concentration.

Inhibition of amyloid beta toxicity in zebrafish with a chaperone-gold nanoparticle dual strategy

Inhibition of hIAPP Amyloid Aggregation and Pancreatic β-Cell Toxicity by OH-Terminated PAMAM Dendrimer.

Interaction of firefly luciferase and silver nanoparticles and its impact on enzyme activity ⬇️

Islet Amyloid Polypeptide Promotes Amyloid-beta Aggregation by Binding-induced Helix-unfolding of the Amyloidogenic Core

Labeling native bacterial RNA in live cells

Local unfolding of Cu, Zn superoxide dismutase monomer determines the morphology of fibrillar aggregates

Lysophosphatidylcholine modulates the aggregation of human islet amyloid polypeptide

Mechanism for the alpha-helix to beta-hairpin transition

Mechanistic Insights from Discrete Molecular Dynamics Simulations of Pesticide-Nanoparticle Interactions.

Mitigating Human IAPP Amyloidogenesis In Vivo with Chiral Silica Nanoribbons

Modeling backbone flexibility improves protein stability estimation.

Modulating protein amyloid aggregation with nanomaterials.

Molecular dynamics simulation of amyloid beta dimer formation

Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism

Molecular origin of polyglutamine aggregation in neurodegenerative diseases

Multiple folding pathways of the SH3 domain

Multiscale modeling of nucleosome dynamics

N-terminal strands of filamin Ig domains act as a conformational switch under biological forces

NanoEHS beyond Toxicity - Focusing on Biocorona

Nanoscale inhibition of polymorphic and ambidextrous IAPP amyloid aggregation with small molecules

Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics

New Insights into FAK Signaling and Localization Based on Detection of a FAT Domain Folding Intermediate

New models of Tetrahymena telomerase RNA from experimentally derived constraints and modeling

Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-like β-Sandwich Proteins

Novel application of a perturbed photonic crystal: High-quality filter

Nucleation of β-rich oligomers and β-barrels in the early aggregation of human islet amyloid polypeptide

On the significance of an RNA tertiary structure prediction

PAMAM dendrimers and graphene: materials for removing aromatic contaminants from water

Parallel folding pathways in the SH3 domain protein

Physical and Toxicological Profiles of Human IAPP Amyloids and Plaques