Lista de obras - Wenjun Zheng - Dominio Público Uruguay

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

artículo científico publicado en 2015

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

artículo científico publicado en 2003

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

artículo científico publicado en 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 ⬇️

artículo científico publicado el 20 de diciembre de 2011

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

artículo científico publicado en 2011

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

artículo científico publicado en 2014

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

artículo científico publicado el 14 de octubre de 2011

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

artículo científico publicado en 2013

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

artículo científico publicado en 2012

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

artículo científico publicado en 2007

Analysis of protein conformational transitions using elastic network model.

artículo científico publicado en 2014

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

artículo científico publicado en 2010

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

artículo científico publicado en 2009

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

artículo científico publicado en 2012

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

artículo científico publicado el 21 de abril de 2012

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

artículo científico publicado el 16 de mayo de 2011

Computer modeling of helicases using elastic network model

artículo científico publicado en 2010

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

artículo científico publicado en 2009

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

artículo científico publicado en 2021

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

artículo científico publicado en 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.

artículo científico publicado en 2015

Electrostatically biased binding of kinesin to microtubules

artículo científico publicado en 2011

Evidence of protein collective motions on the picosecond timescale

artículo científico publicado en 2011

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

artículo científico publicado en 2005

Functional differences between neurotransmitter binding sites of muscle acetylcholine receptors.

artículo científico publicado en 2014

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.

artículo científico publicado en 2014

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

artículo científico

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

artículo científico publicado en 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

artículo científico publicado en 2009

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

artículo científico publicado en 2006

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

artículo científico publicado en 2006

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

artículo científico publicado en 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

artículo científico publicado en 2009

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

artículo científico publicado en 2010

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

artículo científico publicado en 2020

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

artículo científico publicado en 2010

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

artículo científico publicado en 2016

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

artículo científico publicado en 2013

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

artículo científico publicado en 2015

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

artículo científico publicado en 2005

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

artículo científico publicado en 2011

Protein conformational transitions explored by mixed elastic network models

artículo científico publicado en 2007

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

artículo científico publicado en 2002

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

artículo científico publicado en 2012

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

artículo científico publicado en 2015

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

artículo científico publicado en 2007

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

artículo científico publicado en 2014

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

artículo científico publicado en 2008

Lista de obras de 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