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The Applications of Molecular Dynamics Simulation in Studying Protein Structure and Dynamics

Current medicinal chemistry, 2024-01, Vol.31 (20), p.2839-2840

2024

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Molecular Mechanism of Tau Misfolding and Aggregation: Insights from Molecular Dynamics Simulation

Current medicinal chemistry, 2024-01, Vol.31 (20), p.2855-2871

2024

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The molecular mechanism of bisphenol A (BPA) as an endocrine disruptor by interacting with nuclear receptors: insights from molecular dynamics (MD) simulations

PloS one, 2015-03, Vol.10 (3), p.e0120330-e0120330

2015

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Influence of Interface Structure on the Properties of ZnO/Graphene Composites: A Theoretical Study by Density Functional Theory Calculations

Journal of physical chemistry. C, 2013-05, Vol.117 (20), p.10536-10544

2013

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A novel UBE2T inhibitor suppresses Wnt/β-catenin signaling hyperactivation and gastric cancer progression by blocking RACK1 ubiquitination

Oncogene, 2021-02, Vol.40 (5), p.1027-1042

2021

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Revealing the Interaction Mechanism between Mycobacterium tuberculosis GyrB and Novobiocin, SPR719 through Binding Thermodynamics and Dissociation Kinetics Analysis

International journal of molecular sciences, 2024-04, Vol.25 (7), p.3764

2024

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Enhanced photocatalytic properties of titania-graphene nanocomposites: a density functional theory study

Physical chemistry chemical physics : PCCP, 2013-04, Vol.15 (16), p.625-633

2013

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Binding Thermodynamics and Dissociation Kinetics Analysis Uncover the Key Structural Motifs of Phenoxyphenol Derivatives as the Direct InhA Inhibitors and the Hotspot Residues of InhA

International journal of molecular sciences, 2022-09, Vol.23 (17), p.10102

2022

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Ligand recognition and allosteric regulation of DRD1-Gs signaling complexes

Cell, 2021-02, Vol.184 (4), p.943-956.e18

2021

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Introducing block design in graph neural networks for molecular properties prediction

Chemical engineering journal (Lausanne, Switzerland : 1996), 2021-06, Vol.414, p.128817, Article 128817

2021

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QSAR study of selective ligands for the thyroid hormone receptor β

Bioorganic & medicinal chemistry, 2007-08, Vol.15 (15), p.5251-5261

2007

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Versatile Self-Assembly of Triblock Peptides into Stable Collagen Mimetic Heterotrimers

International journal of molecular sciences, 2024-06, Vol.25 (12), p.6550

2024

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Computational study on the unbinding pathways of B-RAF inhibitors and its implication for the difference of residence time: insight from random acceleration and steered molecular dynamics simulations

Physical chemistry chemical physics : PCCP, 2016-02, Vol.18 (7), p.5622-5629

2016

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Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM-GBSA calculation

Journal of computational chemistry, 2011-10, Vol.32 (13), p.2800-2809

2011

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Editorial: Antioxidants and inflammatory immune-related diseases

Frontiers in immunology, 2024-08, Vol.15, p.1476887

2024

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Molecular Dynamics Simulation and Free Energy Calculation Studies of the Binding Mechanism of Allosteric Inhibitors with p38α MAP Kinase

Journal of chemical information and modeling, 2011-12, Vol.51 (12), p.3235-3246

2011

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Molecular Dynamics Simulation, Free Energy Calculation and Structure-Based 3D-QSAR Studies of B-RAF Kinase Inhibitors

Journal of chemical information and modeling, 2011-03, Vol.51 (3), p.680-692

2011

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Molecular Basis of the Interaction for an Essential Subunit PA−PB1 in Influenza Virus RNA Polymerase: Insights from Molecular Dynamics Simulation and Free Energy Calculation

Molecular pharmaceutics, 2010-02, Vol.7 (1), p.75-85

2010

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Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites

Nature communications, 2024-08, Vol.15 (1), p.7348-20

2024

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Insights into the molecular mechanism of positive cooperativity between partial agonist MK-8666 and full allosteric agonist AP8 of hGPR40 by Gaussian accelerated molecular dynamics (GaMD) simulations

Computational and structural biotechnology journal, 2021-01, Vol.19, p.3978-3989

2021

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The prediction of protein-ligand unbinding for modern drug discovery

Expert opinion on drug discovery, 2022-02, Vol.17 (2), p.191-205

2022

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Molecular modeling and residue interaction network studies on the mechanism of binding and resistance of the HCV NS5B polymerase mutants to VX-222 and ANA598

Antiviral research, 2014-04, Vol.104, p.40-51

2014

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Deciphering the Effect of Lysine Acetylation on the Misfolding and Aggregation of Human Tau Fragment 171IPAKTPPAPK180 Using Molecular Dynamic Simulation and the Markov State Model

International journal of molecular sciences, 2022-02, Vol.23 (5), p.2399

2022

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Discovery of Novel HPK1 Inhibitors Through Structure-Based Virtual Screening

Frontiers in pharmacology, 2022-03, Vol.13, p.850855

2022

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Exploring the influence of EGCG on the β-sheet-rich oligomers of human islet amyloid polypeptide (hIAPP1-37) and identifying its possible binding sites from molecular dynamics simulation

PloS one, 2014-04, Vol.9 (4), p.e94796-e94796

2014

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The Applications of Molecular Dynamics Simulation in Studying Protein Structure and Dynamics

Molecular Mechanism of Tau Misfolding and Aggregation: Insights from Molecular Dynamics Simulation

The molecular mechanism of bisphenol A (BPA) as an endocrine disruptor by interacting with nuclear receptors: insights from molecular dynamics (MD) simulations

Influence of Interface Structure on the Properties of ZnO/Graphene Composites: A Theoretical Study by Density Functional Theory Calculations

A novel UBE2T inhibitor suppresses Wnt/β-catenin signaling hyperactivation and gastric cancer progression by blocking RACK1 ubiquitination

Revealing the Interaction Mechanism between Mycobacterium tuberculosis GyrB and Novobiocin, SPR719 through Binding Thermodynamics and Dissociation Kinetics Analysis

Enhanced photocatalytic properties of titania-graphene nanocomposites: a density functional theory study

Binding Thermodynamics and Dissociation Kinetics Analysis Uncover the Key Structural Motifs of Phenoxyphenol Derivatives as the Direct InhA Inhibitors and the Hotspot Residues of InhA

Ligand recognition and allosteric regulation of DRD1-Gs signaling complexes

Introducing block design in graph neural networks for molecular properties prediction

QSAR study of selective ligands for the thyroid hormone receptor β

Versatile Self-Assembly of Triblock Peptides into Stable Collagen Mimetic Heterotrimers

Computational study on the unbinding pathways of B-RAF inhibitors and its implication for the difference of residence time: insight from random acceleration and steered molecular dynamics simulations

Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM-GBSA calculation

Editorial: Antioxidants and inflammatory immune-related diseases

Molecular Dynamics Simulation and Free Energy Calculation Studies of the Binding Mechanism of Allosteric Inhibitors with p38α MAP Kinase

Molecular Dynamics Simulation, Free Energy Calculation and Structure-Based 3D-QSAR Studies of B-RAF Kinase Inhibitors

Molecular Basis of the Interaction for an Essential Subunit PA−PB1 in Influenza Virus RNA Polymerase: Insights from Molecular Dynamics Simulation and Free Energy Calculation

Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites

Insights into the molecular mechanism of positive cooperativity between partial agonist MK-8666 and full allosteric agonist AP8 of hGPR40 by Gaussian accelerated molecular dynamics (GaMD) simulations

The prediction of protein-ligand unbinding for modern drug discovery

Molecular modeling and residue interaction network studies on the mechanism of binding and resistance of the HCV NS5B polymerase mutants to VX-222 and ANA598

Deciphering the Effect of Lysine Acetylation on the Misfolding and Aggregation of Human Tau Fragment 171IPAKTPPAPK180 Using Molecular Dynamic Simulation and the Markov State Model

Discovery of Novel HPK1 Inhibitors Through Structure-Based Virtual Screening

Exploring the influence of EGCG on the β-sheet-rich oligomers of human islet amyloid polypeptide (hIAPP1-37) and identifying its possible binding sites from molecular dynamics simulation

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