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APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling

Nature communications, 2021-01, Vol.12 (1), p.601-601, Article 601

2021

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On the Molecular Origins of Biomass Recalcitrance: The Interaction Network and Solvation Structures of Cellulose Microfibrils

The journal of physical chemistry. B, 2010-10, Vol.114 (42), p.13333-13341

2010

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The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

The Journal of chemical physics, 2008-06, Vol.128 (24), p.244114-244114-11

2008

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Dissecting Force Interactions in Cellulose Deconstruction Reveals the Required Solvent Versatility for Overcoming Biomass Recalcitrance

Journal of the American Chemical Society, 2011-09, Vol.133 (35), p.14033-14041

2011

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LWD-TCP complex activates the morning gene CCA1 in Arabidopsis

Nature communications, 2016-10, Vol.7 (1), p.13181-13181, Article 13181

2016

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The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

The Journal of chemical physics, 2008-06, Vol.128 (24), p.244115-244115

2008

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Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids

Chemical science (Cambridge), 2020-05, Vol.11 (19), p.4969-4979

2020

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Thermodynamics of Cellulose Solvation in Water and the Ionic Liquid 1-Butyl-3-Methylimidazolim Chloride

The journal of physical chemistry. B, 2011-11, Vol.115 (46), p.13433-13440

2011

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Coarse-Grained Free Energy Functions for Studying Protein Conformational Changes: A Double-Well Network Model

Biophysical journal, 2007-12, Vol.93 (11), p.3860-3871

2007

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An incoherent feed-forward loop switches the Arabidopsis clock rapidly between two hysteretic states

Scientific reports, 2018-09, Vol.8 (1), p.13944-16, Article 13944

2018

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Structural basis for overhang excision and terminal unwinding of DNA duplexes by TREX1

PLoS biology, 2018-05, Vol.16 (5), p.e2005653-e2005653

2018

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Illuminating the mechanistic roles of enzyme conformational dynamics

Proceedings of the National Academy of Sciences - PNAS, 2007-11, Vol.104 (46), p.18055-18060

2007

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Statistical learning of protein elastic network from positional covariance matrix

Computational and structural biotechnology journal, 2023-01, Vol.21, p.2524-2535

2023

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Coarse-Grained Modeling of the Actin Filament Derived from Atomistic-Scale Simulations

Biophysical journal, 2006-03, Vol.90 (5), p.1572-1582

2006

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Entropy of cellulose dissolution in water and in the ionic liquid 1-butyl-3-methylimidazolim chloride

Physical chemistry chemical physics : PCCP, 2012-06, Vol.14 (23), p.8425-8430

2012

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On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

Biophysical journal, 2010-11, Vol.99 (10), p.3420-3429

2010

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Importance of Internal Porosity for Glucan Adsorption in Mesoporous Carbon Materials

Langmuir, 2015-07, Vol.31 (26), p.7288-7295

2015

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Expectation-Maximization of the Potential of Mean Force and Diffusion Coefficient in Langevin Dynamics from Single Molecule FRET Data Photon by Photon

The journal of physical chemistry. B, 2013-12, Vol.117 (49), p.15591-15605

2013

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Basal leakage in oscillation: Coupled transcriptional and translational control using feed-forward loops

PLoS computational biology, 2020-09, Vol.16 (9), p.e1007740-e1007740

2020

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Kinetic Modeling at Single-Molecule Resolution Elucidates the Mechanisms of Cellulase Synergy

ACS catalysis, 2014-07, Vol.4 (7), p.2216-2225

2014

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Allostery of Actin Filaments: Molecular Dynamics Simulations and Coarse-Grained Analysis

Proceedings of the National Academy of Sciences - PNAS, 2005-09, Vol.102 (37), p.13111-13116

2005

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Mechanical couplings of protein backbone and side chains exhibit scale-free network properties and specific hotspots for function

Computational and structural biotechnology journal, 2021-01, Vol.19, p.5309-5320

2021

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Understanding APE1 cellular functions by the structural preference of exonuclease activities

Computational and structural biotechnology journal, 2021-01, Vol.19, p.3682-3691

2021

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Trajectory Statistical Learning of the Potential Mean of Force and Diffusion Coefficient from Molecular Dynamics Simulations

The journal of physical chemistry. B, 2024-01, Vol.128 (1), p.56-66

2024

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Intrinsic Bending and Structural Rearrangement of Tubulin Dimer: Molecular Dynamics Simulations and Coarse-Grained Analysis

Biophysical journal, 2008-09, Vol.95 (5), p.2487-2499

2008

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APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling

On the Molecular Origins of Biomass Recalcitrance: The Interaction Network and Solvation Structures of Cellulose Microfibrils

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

Dissecting Force Interactions in Cellulose Deconstruction Reveals the Required Solvent Versatility for Overcoming Biomass Recalcitrance

LWD-TCP complex activates the morning gene CCA1 in Arabidopsis

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids

Thermodynamics of Cellulose Solvation in Water and the Ionic Liquid 1-Butyl-3-Methylimidazolim Chloride

Coarse-Grained Free Energy Functions for Studying Protein Conformational Changes: A Double-Well Network Model

An incoherent feed-forward loop switches the Arabidopsis clock rapidly between two hysteretic states

Structural basis for overhang excision and terminal unwinding of DNA duplexes by TREX1

Illuminating the mechanistic roles of enzyme conformational dynamics

Statistical learning of protein elastic network from positional covariance matrix

Coarse-Grained Modeling of the Actin Filament Derived from Atomistic-Scale Simulations

Entropy of cellulose dissolution in water and in the ionic liquid 1-butyl-3-methylimidazolim chloride

On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

Importance of Internal Porosity for Glucan Adsorption in Mesoporous Carbon Materials

Expectation-Maximization of the Potential of Mean Force and Diffusion Coefficient in Langevin Dynamics from Single Molecule FRET Data Photon by Photon

Basal leakage in oscillation: Coupled transcriptional and translational control using feed-forward loops

Kinetic Modeling at Single-Molecule Resolution Elucidates the Mechanisms of Cellulase Synergy

Allostery of Actin Filaments: Molecular Dynamics Simulations and Coarse-Grained Analysis

Mechanical couplings of protein backbone and side chains exhibit scale-free network properties and specific hotspots for function

Understanding APE1 cellular functions by the structural preference of exonuclease activities

Trajectory Statistical Learning of the Potential Mean of Force and Diffusion Coefficient from Molecular Dynamics Simulations

Intrinsic Bending and Structural Rearrangement of Tubulin Dimer: Molecular Dynamics Simulations and Coarse-Grained Analysis

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