List of works - Xuhui Huang

8-Oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II

scientific article published on 04 February 2019

A Flexible Domain-Domain Hinge Promotes an Induced-fit Dominant Mechanism for the Loading of Guide-DNA into Argonaute Protein in Thermus thermophilus

scientific article

A deep learning framework to predict binding preference of RNA constituents on protein surface

scientific article published on 30 October 2019

A fast parallel clustering algorithm for molecular simulation trajectories

scientific article published on 20 September 2012

A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase

scientific article published on 01 September 2021

A role for both conformational selection and induced fit in ligand binding by the LAO protein

scientific article

A tetraphenylethylene core-based 3D structure small molecular acceptor enabling efficient non-fullerene organic solar cells

article

A theoretical study on the dynamics of light harvesting in the dimeric photosystem II core complex: regulation and robustness of energy transfer pathways

scientific article published on 01 July 2019

A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase

scientific article

AIEgen-based theranostic system: targeted imaging of cancer cells and adjuvant amplification of antitumor efficacy of paclitaxel

scientific article

Achieving enhanced cell penetration of short conformationally constrained peptides through amphiphilicity tuning.

scientific article published on 13 September 2017

Adaptive partitioning by local density-peaks: An efficient density-based clustering algorithm for analyzing molecular dynamics trajectories

scientific article published on 21 November 2016

Aggregation-Induced-Emission-Active Macrocycle Exhibiting Analogous Triply and Singly Twisted Möbius Topologies

scientific article published on 14 July 2015

Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA.

scientific article published on 20 February 2018

An efficient Bayesian kinetic lumping algorithm to identify metastable conformational states via Gibbs sampling

scientific article published on 01 August 2018

Application of Markov State Models to simulate long timescale dynamics of biological macromolecules.

scientific article published in January 2014

Automatic state partitioning for multibody systems (APM): an efficient algorithm for constructing Markov state models to elucidate conformational dynamics of multibody systems

scientific article published on 23 December 2014

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue

scientific article

Ca2+-Induced Rigidity Change of the Myosin VIIa IQ Motif-Single α Helix Lever Arm Extension

scientific article published on 24 February 2017

Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis.

scientific article

Conformational selection turns on phenylalanine hydroxylase

scientific article published in Journal of Biological Chemistry

Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands.

scientific article published on 24 June 2016

Constructing kinetic models to elucidate structural dynamics of a complete RNA polymerase II elongation cycle.

scientific article published on 5 December 2014

Controlling the Integration of Polyvinylpyrrolidone onto Substrate by Quartz Crystal Microbalance with Dissipation To Achieve Excellent Protein Resistance and Detoxification

scientific article published in July 2016

Crystallographic Snapshots of Class A β-Lactamase Catalysis Reveal Structural Changes That Facilitate β-Lactam Hydrolysis

scientific article published on 18 January 2017

DNA-Encoded Dynamic Chemical Library and Its Applications in Ligand Discovery

scientific article published on 09 November 2018

Dewetting transitions in protein cavities

scientific article published on June 2010

Dramatic Differences in Aggregation-Induced Emission and Supramolecular Polymerizability of Tetraphenylethene-Based Stereoisomers

scientific article published on 10 July 2017

Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre

scientific article

Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation.

scientific article published on 17 October 2013

Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II.

scientific article published on 24 January 2012

Dynamics of the conformational transitions during the dimerization of an intrinsically disordered peptide: a case study on the human islet amyloid polypeptide fragment.

scientific article published on 19 October 2016

Elucidating dominant pathways of the nano-particle self-assembly process.

scientific article

Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models

scientific article published on 18 March 2016

Elucidation of the conformational dynamics of multi-body systems by construction of Markov state models

scientific article published on 17 June 2016

Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states.

scientific article published in April 2016

Force field development for cofactors in the photosystem II.

scientific article published on 8 June 2012

Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation

scientific article

Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution

scientific article published on 7 April 2016

Harnessing complexity in molecular self-assembly using computer simulations

scientific article published on 26 February 2018

Hierarchical Nyström methods for constructing Markov state models for conformational dynamics

scientific article published in May 2013

Impact of template backbone heterogeneity on RNA polymerase II transcription.

scientific article

Improving the productivity of monodisperse polyhedral cages by the rational design of kinetic self-assembly pathways

scientific article published on 01 April 2018

Initiation Complex Structure and Promoter Proofreading

scientific article

Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate

scientific article published on 11 February 2019

Investigating the structural origin of trpzip2 temperature dependent unfolding fluorescence line shape based on a Markov state model simulation

scientific article published on 12 October 2012

Kinetics-Controlled Amphiphile Self-Assembly Processes.

scientific article published on 2 April 2017

Maltose-binding protein effectively stabilizes the partially closed conformation of the ATP-binding cassette transporter MalFGK2.

scientific article published on 7 March 2017

Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement

scientific article published on 16 July 2015

Massively parallel de novo protein design for targeted therapeutics.

scientific article published on 27 September 2017

Mechanism of action of thalassospiramides, a new class of calpain inhibitors

scientific article

Mechanochromism: Multifunctional AIEgens: Ready Synthesis, Tunable Emission, Mechanochromism, Mitochondrial, and Bacterial Imaging (Adv. Funct. Mater. 1/2018)

Millisecond dynamics of RNA polymerase II translocation at atomic resolution

scientific article

Molecular mechanisms of RNA polymerase II transcription elongation elucidated by kinetic network models.

scientific article published on 2 February 2018

Monitoring and Inhibition of Insulin Fibrillation by a Small Organic Fluorogen with Aggregation-Induced Emission Characteristics

article

Multiscale modeling of macromolecular biosystems

scientific article published on 06 January 2012

Network models for molecular kinetics and their initial applications to human health

scientific article

Non-aromatic annulene-based aggregation-induced emission system via aromaticity reversal process

scientific article published on 04 July 2019

On the advantages of exploiting memory in Markov state models for biomolecular dynamics

scientific article published on 01 July 2020

Path lumping: An efficient algorithm to identify metastable path channels for conformational dynamics of multi-body systems

scientific article

Poly(l-lysine)-graft-folic acid-coupled poly(2-methyl-2-oxazoline) (PLL-g-PMOXA-c-FA): a bioactive copolymer for specific targeting to folate receptor-positive cancer cells.

scientific article

Quantitative comparison of alternative methods for coarse-graining biological networks

scientific article (publication date: 28 September 2013)

Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysis

scientific article (publication date: August 2014)

RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription

scientific article

Real-time monitoring of hydrophobic aggregation reveals a critical role of cooperativity in hydrophobic effect

scientific article

Reduced Intramolecular Twisting Improves the Performance of 3D Molecular Acceptors in Non-Fullerene Organic Solar Cells

article

Reference interaction site model with hydrophobicity induced density inhomogeneity: An analytical theory to compute solvation properties of large hydrophobic solutes in the mixture of polyatomic solvent molecules.

scientific article published on August 2015

Role of 1’-Ribose Cyano Substitution for Remdesivir to Effectively Inhibit both Nucleotide Addition and Proofreading in SARS-CoV-2 Viral RNA Replication

scientific article published on 28 April 2020

Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach

article

Single-Molecule Investigations of Conformation Adaptation of Porphyrins on Surfaces.

scientific article

Specific and Quantitative Detection of Albumin in Biological Fluids by Tetrazolate-Functionalized Water-Soluble AIEgens

scientific article published on 07 August 2019

Stapling of unprotected helical peptides via photo-induced intramolecular thiol-yne hydrothiolation.

scientific article published on 5 February 2016

Strand-specific (asymmetric) contribution of phosphodiester linkages on RNA polymerase II transcriptional efficiency and fidelity.

scientific article

Structural Basis of Transcription: Backtracked RNA Polymerase II at 3.4 Angstrom Resolution

scientific article

Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes

scientific article (publication date: July 2015)

Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator cross-talk.

scientific article

Structural insight into RNA hairpin folding intermediates

scientific article published on July 2008

Synaptic Targeting and Function of SAPAPs Mediated by Phosphorylation-Dependent Binding to PSD-95 MAGUKs

scientific article published in December 2017

TAPS: A traveling-salesman based automated path searching method for functional conformational changes of biological macromolecules

scientific article published on 01 March 2019

Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models

scientific article published on 20 August 2020

Temperature-dependent kinetic pathways of heterogeneous ice nucleation competing between classical and non-classical nucleation

scientific article published on 16 August 2021

Three-site and five-site fixed-charge water models compatible with AMOEBA force field

scientific article published on 24 January 2020

Topological methods for exploring low-density states in biomolecular folding pathways

scientific article published on April 2009

Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II

scientific article published on 17 June 2021

Two symmetric arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage

scientific article published on 27 December 2018

Understanding molecular recognition by kinetic network models constructed from molecular dynamics simulations

scientific article published on January 2014

Understanding the core of RNA interference: The dynamic aspects of Argonaute-mediated processes.

scientific article

Unique Roles of the Non-identical MCM Subunits in DNA Replication Licensing

scientific article

Unraveling the aggregation effect on amorphous phase AIE luminogens: a computational study

scientific article published on 15 July 2016

Using generalized ensemble simulations and Markov state models to identify conformational states

scientific article published on 04 May 2009

Why Do Simple Molecules with "Isolated" Phenyl Rings Emit Visible Light?

scientific article published on 24 October 2017

X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct

scientific article

List of works by Xuhui Huang

8-Oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II

A Flexible Domain-Domain Hinge Promotes an Induced-fit Dominant Mechanism for the Loading of Guide-DNA into Argonaute Protein in Thermus thermophilus

A deep learning framework to predict binding preference of RNA constituents on protein surface

A fast parallel clustering algorithm for molecular simulation trajectories

A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase

A role for both conformational selection and induced fit in ligand binding by the LAO protein

A tetraphenylethylene core-based 3D structure small molecular acceptor enabling efficient non-fullerene organic solar cells

A theoretical study on the dynamics of light harvesting in the dimeric photosystem II core complex: regulation and robustness of energy transfer pathways

A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase

AIEgen-based theranostic system: targeted imaging of cancer cells and adjuvant amplification of antitumor efficacy of paclitaxel

Achieving enhanced cell penetration of short conformationally constrained peptides through amphiphilicity tuning.

Adaptive partitioning by local density-peaks: An efficient density-based clustering algorithm for analyzing molecular dynamics trajectories

Aggregation-Induced-Emission-Active Macrocycle Exhibiting Analogous Triply and Singly Twisted Möbius Topologies

Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA.

An efficient Bayesian kinetic lumping algorithm to identify metastable conformational states via Gibbs sampling

Application of Markov State Models to simulate long timescale dynamics of biological macromolecules.

Automatic state partitioning for multibody systems (APM): an efficient algorithm for constructing Markov state models to elucidate conformational dynamics of multibody systems

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue

Ca2+-Induced Rigidity Change of the Myosin VIIa IQ Motif-Single α Helix Lever Arm Extension

Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis.

Conformational selection turns on phenylalanine hydroxylase

Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands.

Constructing kinetic models to elucidate structural dynamics of a complete RNA polymerase II elongation cycle.

Controlling the Integration of Polyvinylpyrrolidone onto Substrate by Quartz Crystal Microbalance with Dissipation To Achieve Excellent Protein Resistance and Detoxification

Crystallographic Snapshots of Class A β-Lactamase Catalysis Reveal Structural Changes That Facilitate β-Lactam Hydrolysis

DNA-Encoded Dynamic Chemical Library and Its Applications in Ligand Discovery

Dewetting transitions in protein cavities

Dramatic Differences in Aggregation-Induced Emission and Supramolecular Polymerizability of Tetraphenylethene-Based Stereoisomers

Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre

Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation.

Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II.

Dynamics of the conformational transitions during the dimerization of an intrinsically disordered peptide: a case study on the human islet amyloid polypeptide fragment.

Elucidating dominant pathways of the nano-particle self-assembly process.

Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models

Elucidation of the conformational dynamics of multi-body systems by construction of Markov state models

Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states.

Force field development for cofactors in the photosystem II.

Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation

Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution

Harnessing complexity in molecular self-assembly using computer simulations

Hierarchical Nyström methods for constructing Markov state models for conformational dynamics

Impact of template backbone heterogeneity on RNA polymerase II transcription.

Improving the productivity of monodisperse polyhedral cages by the rational design of kinetic self-assembly pathways

Initiation Complex Structure and Promoter Proofreading

Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate

Investigating the structural origin of trpzip2 temperature dependent unfolding fluorescence line shape based on a Markov state model simulation

Kinetics-Controlled Amphiphile Self-Assembly Processes.

Maltose-binding protein effectively stabilizes the partially closed conformation of the ATP-binding cassette transporter MalFGK2.

Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement

Massively parallel de novo protein design for targeted therapeutics.

Mechanism of action of thalassospiramides, a new class of calpain inhibitors

Mechanochromism: Multifunctional AIEgens: Ready Synthesis, Tunable Emission, Mechanochromism, Mitochondrial, and Bacterial Imaging (Adv. Funct. Mater. 1/2018)

Millisecond dynamics of RNA polymerase II translocation at atomic resolution

Molecular mechanisms of RNA polymerase II transcription elongation elucidated by kinetic network models.

Monitoring and Inhibition of Insulin Fibrillation by a Small Organic Fluorogen with Aggregation-Induced Emission Characteristics

Multiscale modeling of macromolecular biosystems

Network models for molecular kinetics and their initial applications to human health

Non-aromatic annulene-based aggregation-induced emission system via aromaticity reversal process

On the advantages of exploiting memory in Markov state models for biomolecular dynamics

Path lumping: An efficient algorithm to identify metastable path channels for conformational dynamics of multi-body systems

Poly(l-lysine)-graft-folic acid-coupled poly(2-methyl-2-oxazoline) (PLL-g-PMOXA-c-FA): a bioactive copolymer for specific targeting to folate receptor-positive cancer cells.

Quantitative comparison of alternative methods for coarse-graining biological networks

Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysis

RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription

Real-time monitoring of hydrophobic aggregation reveals a critical role of cooperativity in hydrophobic effect

Reduced Intramolecular Twisting Improves the Performance of 3D Molecular Acceptors in Non-Fullerene Organic Solar Cells

Reference interaction site model with hydrophobicity induced density inhomogeneity: An analytical theory to compute solvation properties of large hydrophobic solutes in the mixture of polyatomic solvent molecules.

Role of 1’-Ribose Cyano Substitution for Remdesivir to Effectively Inhibit both Nucleotide Addition and Proofreading in SARS-CoV-2 Viral RNA Replication

Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach

Single-Molecule Investigations of Conformation Adaptation of Porphyrins on Surfaces.

Specific and Quantitative Detection of Albumin in Biological Fluids by Tetrazolate-Functionalized Water-Soluble AIEgens

Stapling of unprotected helical peptides via photo-induced intramolecular thiol-yne hydrothiolation.

Strand-specific (asymmetric) contribution of phosphodiester linkages on RNA polymerase II transcriptional efficiency and fidelity.

Structural Basis of Transcription: Backtracked RNA Polymerase II at 3.4 Angstrom Resolution

Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes

Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator cross-talk.

Structural insight into RNA hairpin folding intermediates

Synaptic Targeting and Function of SAPAPs Mediated by Phosphorylation-Dependent Binding to PSD-95 MAGUKs

TAPS: A traveling-salesman based automated path searching method for functional conformational changes of biological macromolecules