List of works - Wenjun Zheng

A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation

scientific article published on May 2015

A comparative study of motor-protein motions by using a simple elastic-network model

scientific article published on 29 October 2003

A unification of the elastic network model and the Gaussian network model for optimal description of protein conformational motions and fluctuations

scientific article published on 30 January 2008

Accurate Flexible Fitting of High-Resolution Protein Structures to Small-Angle X-Ray Scattering Data Using a Coarse-Grained Model with Implicit Hydration Shell ⬇️

scientific article published on December 20, 2011

Accurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization

scientific article

All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex.

scientific article

All-atom modeling of anisotropic atomic fluctuations in protein crystal structures ⬇️

scientific article published on October 14, 2011

All-atom molecular dynamics simulations of actin-myosin interactions: a comparative study of cardiac α myosin, β myosin, and fast skeletal muscle myosin.

scientific article published on 13 November 2013

All-atom structural investigation of kinesin-microtubule complex constrained by high-quality cryo-electron-microscopy maps.

scientific article published on 15 June 2012

Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations.

scientific article

Analysis of protein conformational transitions using elastic network model.

scientific article published on January 2014

Anharmonic normal mode analysis of elastic network model improves the modeling of atomic fluctuations in protein crystal structures.

scientific article published on June 2010

Approximate normal mode analysis based on vibrational subsystem analysis with high accuracy and efficiency

scientific article published in May 2009

Coarse-grained and all-atom modeling of structural states and transitions in hemoglobin

scientific article published on 26 October 2012

Coarse-grained modeling of the structural states and transition underlying the powerstroke of dynein motor domain ⬇️

scientific article published on April 21, 2012

Coarse‐grained modeling of conformational transitions underlying the processive stepping of myosin V dimer along filamentous actin ⬇️

scientific article published on May 16, 2011

Computer modeling of helicases using elastic network model

scientific article published in January 2010

Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II

scientific article

Cross-subunit interactions that stabilize open states mediate gating in NMDA receptors

scientific article published on 01 January 2021

Decrypting the sequence of structural events during the gating transition of pentameric ligand-gated ion channels based on an interpolated elastic network model

scientific article (publication date: 2011)

Decrypting the structural, dynamic, and energetic basis of a monomeric kinesin interacting with a tubulin dimer in three ATPase states by all-atom molecular dynamics simulation.

scientific article published on 12 January 2015

Electrostatically biased binding of kinesin to microtubules

scientific article

Evidence of protein collective motions on the picosecond timescale

scientific article

Fold recognition aided by constraints from small angle X-ray scattering data

scientific article

Functional differences between neurotransmitter binding sites of muscle acetylcholine receptors.

scientific article

Heat activation mechanism of TRPV1: New insights from molecular dynamics simulation

scientific article published on 19 February 2019

High-resolution modeling of protein structures based on flexible fitting of low-resolution structural data.

scientific article

Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model

scientific article published on 05 January 2005

Investigating dual Ca2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation

scientific article published on 17 June 2020

Investigating the inter-subunit/subdomain interactions and motions relevant to disease mutations in the N-terminal domain of ryanodine receptors by molecular dynamics simulation

scientific article published on 15 May 2017

Investigating the structural dynamics of the PIEZO1 channel activation and inactivation by coarse-grained modeling

scientific article published on 14 September 2017

Langevin Network Model of Myosin†

article

Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model

scientific article published on 10 July 2009

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations

scholarly article

Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes.

scientific article

Molecular dynamics simulation of tropomyosin bound to actins/myosin in the closed and open states

scientific article published on 23 May 2019

Multiscale modeling of structural dynamics underlying force generation and product release in actomyosin complex

scientific article published in February 2010

Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved

scientific article published on 01 April 2005

Normal-mode-based modeling of allosteric couplings that underlie cyclic conformational transition in F(1) ATPase

scientific article

Optimal modeling of atomic fluctuations in protein crystal structures for weak crystal contact interactions.

scientific article

Predicting cryptic ligand binding sites based on normal modes guided conformational sampling

scientific article published on 26 November 2020

Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model

scientific article published on August 2010

Probing the Energetics of Dynactin Filament Assembly and the Binding of Cargo Adaptor Proteins Using Molecular Dynamics Simulation and Electrostatics-Based Structural Modeling

scientific article published on 15 December 2016

Probing the flexibility of tropomyosin and its binding to filamentous actin using molecular dynamics simulations

scientific article published on October 2013

Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation.

scientific article published on January 2015

Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.

scientific article

Probing the structural and energetic basis of kinesin-microtubule binding using computational alanine-scanning mutagenesis.

scientific article published on 19 September 2011

Protein conformational transitions explored by mixed elastic network models

scientific article published in October 2007

Protein structure prediction constrained by solution X-ray scattering data and structural homology identification.

scientific article

Structure-based simulations of the translocation mechanism of the hepatitis C virus NS3 helicase along single-stranded nucleic acid.

scientific article

Toward decrypting the allosteric mechanism of the ryanodine receptor based on coarse-grained structural and dynamic modeling

scientific article published on 22 October 2015

Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model

scientific article published on June 2007

Unzipping of neuronal snare protein with steered molecular dynamics occurs in three steps

scientific article published on 31 July 2014

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

scientific article published on December 2008

List of works by Wenjun Zheng

A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation

A comparative study of motor-protein motions by using a simple elastic-network model

A unification of the elastic network model and the Gaussian network model for optimal description of protein conformational motions and fluctuations

Accurate Flexible Fitting of High-Resolution Protein Structures to Small-Angle X-Ray Scattering Data Using a Coarse-Grained Model with Implicit Hydration Shell ⬇️

Accurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization

All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex.

All-atom modeling of anisotropic atomic fluctuations in protein crystal structures ⬇️

All-atom molecular dynamics simulations of actin-myosin interactions: a comparative study of cardiac α myosin, β myosin, and fast skeletal muscle myosin.

All-atom structural investigation of kinesin-microtubule complex constrained by high-quality cryo-electron-microscopy maps.

Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations.

Analysis of protein conformational transitions using elastic network model.

Anharmonic normal mode analysis of elastic network model improves the modeling of atomic fluctuations in protein crystal structures.

Approximate normal mode analysis based on vibrational subsystem analysis with high accuracy and efficiency

Coarse-grained and all-atom modeling of structural states and transitions in hemoglobin

Coarse-grained modeling of the structural states and transition underlying the powerstroke of dynein motor domain ⬇️

Coarse‐grained modeling of conformational transitions underlying the processive stepping of myosin V dimer along filamentous actin ⬇️

Computer modeling of helicases using elastic network model

Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II

Cross-subunit interactions that stabilize open states mediate gating in NMDA receptors

Decrypting the sequence of structural events during the gating transition of pentameric ligand-gated ion channels based on an interpolated elastic network model

Decrypting the structural, dynamic, and energetic basis of a monomeric kinesin interacting with a tubulin dimer in three ATPase states by all-atom molecular dynamics simulation.

Electrostatically biased binding of kinesin to microtubules

Evidence of protein collective motions on the picosecond timescale

Fold recognition aided by constraints from small angle X-ray scattering data

Functional differences between neurotransmitter binding sites of muscle acetylcholine receptors.

Heat activation mechanism of TRPV1: New insights from molecular dynamics simulation

High-resolution modeling of protein structures based on flexible fitting of low-resolution structural data.

Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model

Investigating dual Ca2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation

Investigating the inter-subunit/subdomain interactions and motions relevant to disease mutations in the N-terminal domain of ryanodine receptors by molecular dynamics simulation

Investigating the structural dynamics of the PIEZO1 channel activation and inactivation by coarse-grained modeling

Langevin Network Model of Myosin†

Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations

Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes.

Molecular dynamics simulation of tropomyosin bound to actins/myosin in the closed and open states

Multiscale modeling of structural dynamics underlying force generation and product release in actomyosin complex

Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved

Normal-mode-based modeling of allosteric couplings that underlie cyclic conformational transition in F(1) ATPase

Optimal modeling of atomic fluctuations in protein crystal structures for weak crystal contact interactions.

Predicting cryptic ligand binding sites based on normal modes guided conformational sampling

Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model

Probing the Energetics of Dynactin Filament Assembly and the Binding of Cargo Adaptor Proteins Using Molecular Dynamics Simulation and Electrostatics-Based Structural Modeling

Probing the flexibility of tropomyosin and its binding to filamentous actin using molecular dynamics simulations

Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation.

Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.

Probing the structural and energetic basis of kinesin-microtubule binding using computational alanine-scanning mutagenesis.

Protein conformational transitions explored by mixed elastic network models

Protein structure prediction constrained by solution X-ray scattering data and structural homology identification.

Structure-based simulations of the translocation mechanism of the hepatitis C virus NS3 helicase along single-stranded nucleic acid.

Toward decrypting the allosteric mechanism of the ryanodine receptor based on coarse-grained structural and dynamic modeling

Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model

Unzipping of neuronal snare protein with steered molecular dynamics occurs in three steps

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit