AIMC Topic: Molecular Dynamics Simulation

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Investigating PCB degradation by indigenous fungal strains isolated from the transformer oil-contaminated site: degradation kinetics, Bayesian network, artificial neural networks, QSAR with DFT, molecular docking, and molecular dynamics simulation.

Environmental science and pollution research international Sep 6, 2024
The widespread prevalence of polychlorinated biphenyls (PCBs) in the environment has raised major concerns due to the associated risks to human health, wildlife, and ecological systems. Here, we investigated the degradation kinetics, Bayesian network...
Polychlorinated Biphenyls Quantitative Structure-Activity Relationship Bayes Theorem Soil Pollutants Kinetics Molecular Dynamics Simulation Biodegradation, Environmental Fungi Neural Networks, Computer Molecular Docking Simulation
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Combining network pharmacology, machine learning, molecular docking and molecular dynamic to explore the mechanism of Chufeng Qingpi decoction in treating schistosomiasis.

Frontiers in cellular and infection microbiology Sep 6, 2024
BACKGROUND: Although the Chufeng Qingpi Decoction (CQD) has demonstrated clinical effectiveness in the treatment of schistosomiasis, the precise active components and the underlying mechanisms of its therapeutic action remain elusive. To achieve a pr...
Network Pharmacology Protein Interaction Maps Computational Biology Drugs, Chinese Herbal Humans Quercetin Machine Learning Molecular Dynamics Simulation Molecular Docking Simulation Flavanones Tumor Suppressor Protein p53 Kaempferols Schistosomiasis
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Machine learning, network pharmacology, and molecular dynamics reveal potent cyclopeptide inhibitors against dengue virus proteins.

Molecular diversity Sep 4, 2024
The dengue virus is a major global health hazard responsible for an estimated 390 million diseases yearly. This study focused on identifying cyclopeptide inhibitors for envelope structural proteins E, NS1, NS3, and NS5. Additionally, 5579 cyclopeptid...
Molecular Docking Simulation Antiviral Agents Protein Binding Quantitative Structure-Activity Relationship Machine Learning Molecular Dynamics Simulation Viral Nonstructural Proteins Thermodynamics Dengue Virus Viral Proteins Peptides, Cyclic
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A Deep Learning Approach to Uncover Voltage-Gated Ion Channels' Intermediate States.

The journal of physical chemistry. B Aug 30, 2024
Owing to recent advancements in cryo-electron microscopy, voltage-gated ion channels have gained a greater comprehension of their structural characteristics. However, a significant enigma remains unsolved for a large majority of these channels: their...
Deep Learning Molecular Dynamics Simulation Protein Conformation Ion Channel Gating Kv1.2 Potassium Channel
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From Static to Dynamic Structures: Improving Binding Affinity Prediction with Graph-Based Deep Learning.

Advanced science (Weinheim, Baden-Wurttemberg, Germany) Aug 29, 2024
Accurate prediction of protein-ligand binding affinities is an essential challenge in structure-based drug design. Despite recent advances in data-driven methods for affinity prediction, their accuracy is still limited, partially because they only ta...
Proteins Molecular Dynamics Simulation Ligands Thermodynamics HSP90 Heat-Shock Proteins Drug Design Deep Learning Protein Binding
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Conformations of KRAS4B Affected by Its Partner Binding and G12C Mutation: Insights from GaMD Trajectory-Image Transformation-Based Deep Learning.

Journal of chemical information and modeling Aug 28, 2024
Binding of partners and mutations highly affects the conformational dynamics of KRAS4B, which is of significance for deeply understanding its function. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) and prin...
Humans Normal Distribution Proto-Oncogene Proteins p21(ras) Mutation Molecular Dynamics Simulation Protein Conformation Deep Learning Protein Binding Principal Component Analysis
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Chemical analogue based drug design for cancer treatment targeting PI3K: integrating machine learning and molecular modeling.

Molecular diversity Aug 17, 2024
Cancer is a generic term for a group of disorders defined by uncontrolled cell growth and the potential to invade or spread to other parts of the body. Gene and epigenetic alterations disrupt normal cellular control, leading to abnormal cell prolifer...
Protein Kinase Inhibitors Phosphoinositide-3 Kinase Inhibitors Class Ib Phosphatidylinositol 3-Kinase Phosphatidylinositol 3-Kinases Molecular Dynamics Simulation Ligands Antineoplastic Agents Protein Binding Models, Molecular Humans Molecular Docking Simulation Drug Design Machine Learning Neoplasms
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Identification of mycobacterial Thymidylate kinase inhibitors: a comprehensive pharmacophore, machine learning, molecular docking, and molecular dynamics simulation studies.

Molecular diversity Aug 16, 2024
Thymidylate kinase (TMK) is a pivotal enzyme in Mycobacterium tuberculosis (Mtb), crucial for phosphorylating thymidine monophosphate (dTMP) to thymidine diphosphate (dTDP), thereby playing a critical role in DNA biosynthesis. Dysregulation or inhibi...
Enzyme Inhibitors Protein Kinase Inhibitors Nucleoside-Phosphate Kinase Antitubercular Agents Molecular Dynamics Simulation Mycobacterium tuberculosis Pharmacophore Machine Learning Molecular Docking Simulation Protein Binding
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Discovery of novel ULK1 inhibitors through machine learning-guided virtual screening and biological evaluation.

Future medicinal chemistry Aug 15, 2024
Build a virtual screening model for ULK1 inhibitors based on artificial intelligence. Build machine learning and deep learning classification models and combine molecular docking and biological evaluation to screen ULK1 inhibitors from 13 million co...
Molecular Docking Simulation Drug Discovery Molecular Structure Humans Machine Learning Intracellular Signaling Peptides and Proteins Autophagy-Related Protein-1 Homolog Molecular Dynamics Simulation Drug Evaluation, Preclinical Protein Kinase Inhibitors
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Navigating the landscape of enzyme design: from molecular simulations to machine learning.

Chemical Society reviews Aug 12, 2024
Global environmental issues and sustainable development call for new technologies for fine chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the alternative to the traditional organic synthesis. However, it is c...
Animals Molecular Dynamics Simulation Biocatalysis Protein Conformation Humans Machine Learning Enzymes Enzyme Activation Substrate Specificity Protein Engineering
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