List of works - Feng Ding

Eris: an automated estimator of protein stability

scientific article published in June 2007

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

scientific article published on July 2008

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

scientific article published on 2 May 2008

Automated minimization of steric clashes in protein structures

scientific article

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

scientific article published on 23 February 2012

Emergence of protein fold families through rational design

scientific article

Engineered allosteric activation of kinases in living cells

scientific article

Mechanism for the alpha-helix to beta-hairpin transition

scientific article

iFoldRNA: three-dimensional RNA structure prediction and folding

scientific article

Modeling backbone flexibility improves protein stability estimation

scientific article

Topological determinants of protein folding

scientific article

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

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

scientific article published on 16 April 2015

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

scientific article

Direct molecular dynamics observation of protein folding transition state ensemble

scientific article

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

scientific article

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

scientific article

On the significance of an RNA tertiary structure prediction

scientific article

Multiscale modeling of nucleosome dynamics

scientific article published on December 2006

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

scientific article published in February 2009

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

scholarly article

Fast complementation of split fluorescent protein triggered by DNA hybridization

scholarly article

Topological Determinants of Protein Domain Swapping

article published in 2006

Molecular origin of polyglutamine aggregation in neurodegenerative diseases

scientific article

Rational design of a ligand-controlled protein conformational switch

scientific article published on 8 April 2013

Three-dimensional RNA structure refinement by hydroxyl radical probing

scientific article

Structural and dynamic determinants of protein-peptide recognition

scientific article

Direct observation of a single nanoparticle-ubiquitin corona formation

scientific article

Discrete molecular dynamics simulations of peptide aggregation

scientific article published on 29 April 2004

Implications of peptide assemblies in amyloid diseases

scientific article

Simple but predictive protein models

article

Harnessing a physiologic mechanism for siRNA delivery with mimetic lipoprotein particles

scientific article published on 5 June 2012

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

scientific article published on 21 December 2011

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

scientific article

Rapid flexible docking using a stochastic rotamer library of ligands

scientific article

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

scientific article published in November 2003

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

scientific article published in Journal of Biological Chemistry

Active nuclear receptors exhibit highly correlated AF-2 domain motions

scientific article

Protein folding: then and now

scientific article

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

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

scientific article

Scaling behavior and structure of denatured proteins

scientific article published in July 2005

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

scientific article published on June 2010

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

scientific article published on 25 January 2016

The Length Dependence of the PolyQ-mediated Protein Aggregation

scientific article published in Journal of Biological Chemistry

Competitive binding of natural amphiphiles with graphene derivatives

scientific article published on 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

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

scientific article

G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase

scientific article

List of works by Feng Ding

Eris: an automated estimator of protein stability

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

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

Automated minimization of steric clashes in protein structures

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

Emergence of protein fold families through rational design

Engineered allosteric activation of kinases in living cells

Mechanism for the alpha-helix to beta-hairpin transition

iFoldRNA: three-dimensional RNA structure prediction and folding

Modeling backbone flexibility improves protein stability estimation

Topological determinants of protein folding

Molecular dynamics simulation of amyloid beta dimer formation

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

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

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

Direct molecular dynamics observation of protein folding transition state ensemble

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

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

On the significance of an RNA tertiary structure prediction

Multiscale modeling of nucleosome dynamics

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

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

Fast complementation of split fluorescent protein triggered by DNA hybridization

Topological Determinants of Protein Domain Swapping

Molecular origin of polyglutamine aggregation in neurodegenerative diseases

Rational design of a ligand-controlled protein conformational switch

Three-dimensional RNA structure refinement by hydroxyl radical probing

Structural and dynamic determinants of protein-peptide recognition

Direct observation of a single nanoparticle-ubiquitin corona formation

Discrete molecular dynamics simulations of peptide aggregation

Implications of peptide assemblies in amyloid diseases

Simple but predictive protein models

Harnessing a physiologic mechanism for siRNA delivery with mimetic lipoprotein particles

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

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

Rapid flexible docking using a stochastic rotamer library of ligands

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

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

Active nuclear receptors exhibit highly correlated AF-2 domain motions

Protein folding: then and now

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

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

Scaling behavior and structure of denatured proteins

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

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

The Length Dependence of the PolyQ-mediated Protein Aggregation

Competitive binding of natural amphiphiles with graphene derivatives

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

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

G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase