AIMC Topic: Molecular Dynamics Simulation

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Synergistic effect of horizontal transfer of antibiotic resistance genes between bacteria exposed to microplastics and per/polyfluoroalkyl substances: An explanation from theoretical methods.

Journal of hazardous materials Apr 8, 2025
Microplastics (MPs) and per/polyfluoroalkyl substances (PFASs), as emerging pollutants widely present in aquatic environments, pose a significant threat to human health through the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs)....
Drug Resistance, Bacterial Bacteria Gene Transfer, Horizontal Microplastics Fluorocarbons Genes, Bacterial Water Pollutants, Chemical Drug Resistance, Microbial Molecular Dynamics Simulation
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QuantumBind-RBFE: Accurate Relative Binding Free Energy Calculations Using Neural Network Potentials.

Journal of chemical information and modeling Apr 8, 2025
Accurate prediction of protein-ligand binding affinities is crucial in drug discovery, particularly during hit-to-lead and lead optimization phases, however, limitations in ligand force fields continue to impact prediction accuracy. In this work, we ...
Ligands Thermodynamics Proteins Molecular Dynamics Simulation Quantum Theory Neural Networks, Computer Protein Binding
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Enhancing the synthesis efficiency of galacto-oligosaccharides of a β-galactosidase from Paenibacillus barengoltzii by engineering the active and distal sites.

Food chemistry Apr 4, 2025
Previously, a glycoside hydrolase (GH) family 2 β-galactosidase (PbBGal2A) from Paenibacillus barengoltzii is characterized for its high transglycosylation capability. Here, the cryo-electron microscopy (cryo-EM) structure of PbBGal2A was determined,...
Bacterial Proteins Molecular Dynamics Simulation Oligosaccharides Galactose Protein Engineering Paenibacillus beta-Galactosidase Biocatalysis Catalytic Domain
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Advancing Molecular Simulations: Merging Physical Models, Experiments, and AI to Tackle Multiscale Complexity.

The journal of physical chemistry letters Apr 3, 2025
Proteins and protein complexes form adaptable networks that regulate essential biochemical pathways and define cell phenotypes through dynamic mechanisms and interactions. Advances in structural biology and molecular simulations have revealed how pro...
Machine Learning Proteins Molecular Dynamics Simulation Protein Conformation Cryoelectron Microscopy
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Integrating deep learning and molecular dynamics simulations for FXR antagonist discovery.

Molecular diversity Apr 2, 2025
Farnesoid X receptor (FXR) is a key regulator of bile acid, lipid, and glucose homeostasis, making it a promising target for treating metabolic diseases. FXR antagonists have shown therapeutic potential in cholestasis, metabolic disorders, and certai...
Hydrophobic and Hydrophilic Interactions Humans Receptors, Cytoplasmic and Nuclear Drug Discovery Thermodynamics Deep Learning Protein Binding Molecular Dynamics Simulation
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Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model.

Cell genomics Apr 1, 2025
Signaling pathway components are well studied, but how they mediate cell-type-specific transcription responses is an unresolved problem. Using the Hippo pathway in mouse trophoblast stem cells as a model, we show that the DNA binding of signaling eff...
Hippo Signaling Pathway YAP-Signaling Proteins TEA Domain Transcription Factors Trophoblasts Enhancer Elements, Genetic Muscle Proteins Transcription Factors Protein Serine-Threonine Kinases Adaptor Proteins, Signal Transducing DNA-Binding Proteins Molecular Dynamics Simulation Phosphoproteins Protein Binding Mice Animals Signal Transduction Deep Learning
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DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials.

Journal of chemical information and modeling Mar 27, 2025
Machine learning potentials (MLPs) have revolutionized molecular simulation by providing efficient and accurate models for predicting atomic interactions. MLPs continue to advance and have had profound impact in applications that include drug discove...
Graph Neural Networks Software Molecular Dynamics Simulation Quantum Theory Neural Networks, Computer
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Discovery and characterization of novel FAK inhibitors for breast cancer therapy via hybrid virtual screening, biological evaluation and molecular dynamics simulations.

Bioorganic chemistry Mar 26, 2025
Focal adhesion kinase (FAK) is a critical drug target implicated in various disease pathways, including hematological malignancies and breast cancer. Therefore, identifying FAK inhibitors with novel scaffolds could offer new opportunities for develop...
Structure-Activity Relationship Molecular Structure Molecular Dynamics Simulation Cell Proliferation Dose-Response Relationship, Drug Drug Screening Assays, Antitumor Focal Adhesion Protein-Tyrosine Kinases Drug Evaluation, Preclinical Protein Kinase Inhibitors Focal Adhesion Kinase 1 Humans Female Breast Neoplasms Molecular Docking Simulation Drug Discovery Antineoplastic Agents
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Machine Learning-Guided Screening and Molecular Docking for Proposing Naturally Derived Drug Candidates Against MERS-CoV 3CL Protease.

International journal of molecular sciences Mar 26, 2025
In this study, we utilized machine learning techniques to identify potential inhibitors of the MERS-CoV 3CL protease. Among the models evaluated, the Random Forest (RF) algorithm exhibited the highest predictive performance, achieving an accuracy of ...
Molecular Dynamics Simulation Catalytic Domain Middle East Respiratory Syndrome Coronavirus Molecular Docking Simulation Humans Protease Inhibitors Drug Discovery Machine Learning Antiviral Agents Coronavirus 3C Proteases
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Insights into phosphorylation-induced influences on conformations and inhibitor binding of CDK6 through GaMD trajectory-based deep learning.

Physical chemistry chemical physics : PCCP Mar 26, 2025
The phosphorylation of residue T177 produces a significant effect on the conformational dynamics of CDK6. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) are applied to explore the molecular mechanism of the ...
Cyclin-Dependent Kinase 6 Humans Deep Learning Protein Binding Protein Conformation Phosphorylation Protein Kinase Inhibitors Molecular Dynamics Simulation Thermodynamics
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