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Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations

Nature communications, 2022-03, Vol.13 (1), p.1661-16, Article 1661

2022

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Molecular Dynamics Simulation Combined with Neural Relationship Inference and Markov Model to Reveal the Relationship between Conformational Regulation and Bioluminescence Properties of Gaussia Luciferase

Molecules (Basel, Switzerland), 2024-08, Vol.29 (17), p.4029

2024

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Probing the Mechanisms of Inhibitors Binding to Presenilin Homologue Using Molecular Dynamics Simulations

Molecules (Basel, Switzerland), 2023-02, Vol.28 (5), p.2076

2023

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Prediction of hyaluronic acid target on sucrase-isomaltase (SI) with reverse docking and molecular dynamics simulations for inhibitors binding to SI

PloS one, 2021-07, Vol.16 (7), p.e0255351-e0255351

2021

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Clustering Analysis, Structure Fingerprint Analysis, and Quantum Chemical Calculations of Compounds from Essential Oils of Sunflower (Helianthus annuus L.) Receptacles

International journal of molecular sciences, 2022-09, Vol.23 (17), p.10169

2022

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Network Pharmacology Combined with Machine Learning to Reveal the Action Mechanism of Licochalcone Intervention in Liver Cancer

International journal of molecular sciences, 2023-11, Vol.24 (21), p.15935

2023

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Specific Substrate Activity of Lotus Root Polyphenol Oxidase: Insights from Gaussian-Accelerated Molecular Dynamics and Markov State Models

International journal of molecular sciences, 2024-09, Vol.25 (18), p.10074

2024

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In Silico Discovery of Anticancer Peptides from Sanghuang

International journal of molecular sciences, 2022-11, Vol.23 (22), p.13682

2022

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Molecular Dynamic Simulations of Bromodomain and Extra-Terminal Protein 4 Bonded to Potent Inhibitors

Molecules (Basel, Switzerland), 2021-12, Vol.27 (1), p.118

2021

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Functionalized Fullerene Potentially Inhibits SARS-CoV-2 Infection by Modulating Spike Protein Conformational Changes

International journal of molecular sciences, 2023-10, Vol.24 (19), p.14471

2023

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Integrating Computational and Experimental Methods to Identify Novel Sweet Peptides from Egg and Soy Proteins

International journal of molecular sciences, 2024-05, Vol.25 (10), p.5430

2024

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Using deep learning and molecular dynamics simulations to unravel the regulation mechanism of peptides as noncompetitive inhibitor of xanthine oxidase

Scientific reports, 2024-01, Vol.14 (1), p.174-174, Article 174

2024

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Mlp4green: A Binary Classification Approach Specifically for Green Odor

International journal of molecular sciences, 2024-03, Vol.25 (6), p.3515

2024

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Molecular Dynamics Simulations Study of the Interactions between Human Dipeptidyl-Peptidase III and Two Substrates

Molecules (Basel, Switzerland), 2021-10, Vol.26 (21), p.6492

2021

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Mulberry Leaf Compounds and Gut Microbiota in Alzheimer's Disease and Diabetes: A Study Using Network Pharmacology, Molecular Dynamics Simulation, and Cellular Assays

International journal of molecular sciences, 2024-04, Vol.25 (7), p.4062

2024

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A Possible Mechanism of Graphene Oxide to Enhance Thermostability of D-Psicose 3-Epimerase Revealed by Molecular Dynamics Simulations

International journal of molecular sciences, 2021-10, Vol.22 (19), p.10813

2021

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Probing inhibition mechanisms of adenosine deaminase by using molecular dynamics simulations

PloS one, 2018-11, Vol.13 (11), p.e0207234-e0207234

2018

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The Antidiabetic Activities of Neocryptotanshinone: Screened by Molecular Docking and Related to the Modulation of PTP1B

Nutrients, 2022-07, Vol.14 (15), p.3031

2022

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Computational Study on the Effect of Inactivating/Activating Mutations on the Inhibition of MEK1 by Trametinib

International journal of molecular sciences, 2020-03, Vol.21 (6), p.2167

2020

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Computer-Aided Screening and Revealing Action Mechanism of Green Tea Polyphenols Intervention in Alzheimer's Disease

Foods, 2023-02, Vol.12 (3), p.635

2023

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Sodium valproate alleviates neurodegeneration in SCA3/MJD via suppressing apoptosis and rescuing the hypoacetylation levels of histone H3 and H4

PloS one, 2013-01, Vol.8 (1), p.e54792

2013

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Theoretical Study on Zearalenol Compounds Binding with Wild Type Zearalenone Hydrolase and V153H Mutant

International journal of molecular sciences, 2018-09, Vol.19 (9), p.2808

2018

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Network pharmacology and experiment indicated that medicinal food homologous components play important roles in insomnia

Food frontiers, 2023-12, Vol.4 (4), p.1859-1877

2023

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Gaussian Accelerated Molecular Dynamics Simulations Investigation on the Mechanism of Angiotensin-Converting Enzyme (ACE) C-Domain Inhibition by Dipeptides

Foods, 2022-01, Vol.11 (3), p.327

2022

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Exploration of Catalytic Selectivity for Aminotransferase (BtrR) Based on Multiple Molecular Dynamics Simulations

International journal of molecular sciences, 2019-03, Vol.20 (5), p.1188

2019

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Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations

Molecular Dynamics Simulation Combined with Neural Relationship Inference and Markov Model to Reveal the Relationship between Conformational Regulation and Bioluminescence Properties of Gaussia Luciferase

Probing the Mechanisms of Inhibitors Binding to Presenilin Homologue Using Molecular Dynamics Simulations

Prediction of hyaluronic acid target on sucrase-isomaltase (SI) with reverse docking and molecular dynamics simulations for inhibitors binding to SI

Clustering Analysis, Structure Fingerprint Analysis, and Quantum Chemical Calculations of Compounds from Essential Oils of Sunflower (Helianthus annuus L.) Receptacles

Network Pharmacology Combined with Machine Learning to Reveal the Action Mechanism of Licochalcone Intervention in Liver Cancer

Specific Substrate Activity of Lotus Root Polyphenol Oxidase: Insights from Gaussian-Accelerated Molecular Dynamics and Markov State Models

In Silico Discovery of Anticancer Peptides from Sanghuang

Molecular Dynamic Simulations of Bromodomain and Extra-Terminal Protein 4 Bonded to Potent Inhibitors

Functionalized Fullerene Potentially Inhibits SARS-CoV-2 Infection by Modulating Spike Protein Conformational Changes

Integrating Computational and Experimental Methods to Identify Novel Sweet Peptides from Egg and Soy Proteins

Using deep learning and molecular dynamics simulations to unravel the regulation mechanism of peptides as noncompetitive inhibitor of xanthine oxidase

Mlp4green: A Binary Classification Approach Specifically for Green Odor

Molecular Dynamics Simulations Study of the Interactions between Human Dipeptidyl-Peptidase III and Two Substrates

Mulberry Leaf Compounds and Gut Microbiota in Alzheimer's Disease and Diabetes: A Study Using Network Pharmacology, Molecular Dynamics Simulation, and Cellular Assays

A Possible Mechanism of Graphene Oxide to Enhance Thermostability of D-Psicose 3-Epimerase Revealed by Molecular Dynamics Simulations

Probing inhibition mechanisms of adenosine deaminase by using molecular dynamics simulations

The Antidiabetic Activities of Neocryptotanshinone: Screened by Molecular Docking and Related to the Modulation of PTP1B

Computational Study on the Effect of Inactivating/Activating Mutations on the Inhibition of MEK1 by Trametinib

Computer-Aided Screening and Revealing Action Mechanism of Green Tea Polyphenols Intervention in Alzheimer's Disease

Sodium valproate alleviates neurodegeneration in SCA3/MJD via suppressing apoptosis and rescuing the hypoacetylation levels of histone H3 and H4

Theoretical Study on Zearalenol Compounds Binding with Wild Type Zearalenone Hydrolase and V153H Mutant

Network pharmacology and experiment indicated that medicinal food homologous components play important roles in insomnia

Gaussian Accelerated Molecular Dynamics Simulations Investigation on the Mechanism of Angiotensin-Converting Enzyme (ACE) C-Domain Inhibition by Dipeptides

Exploration of Catalytic Selectivity for Aminotransferase (BtrR) Based on Multiple Molecular Dynamics Simulations

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