AIMC Topic: Molecular Dynamics Simulation

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Enhancing the understandings on SARS-CoV-2 main protease (M) mutants from molecular dynamics and machine learning.

International journal of biological macromolecules Apr 10, 2025
While star drugs like Paxlovid have shown remarkable performance in combating SARS-CoV-2, we still face serious challenges such as viral mutants and resistance. In this study, we employ a computational framework combining molecular dynamics (MD) simu...
Drug Resistance, Viral Protease Inhibitors Coronavirus 3C Proteases Mutation Molecular Dynamics Simulation Humans Machine Learning COVID-19 SARS-CoV-2 Antiviral Agents
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LEGOLAS: A Machine Learning Method for Rapid and Accurate Predictions of Protein NMR Chemical Shifts.

Journal of chemical theory and computation Apr 10, 2025
This work introduces LEGOLAS, a fully open source TorchANI-based neural network model designed to predict NMR chemical shifts for protein backbone atoms (N, Cα, Cβ, C', HN, Hα). LEGOLAS has been designed to be fast without loss of accuracy, as our mo...
Neural Networks, Computer Nuclear Magnetic Resonance, Biomolecular Machine Learning Escherichia coli Proteins Molecular Dynamics Simulation Escherichia coli Proteins
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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 Water Pollutants, Chemical Fluorocarbons Drug Resistance, Microbial Genes, Bacterial 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 ...
Proteins Molecular Dynamics Simulation Quantum Theory Neural Networks, Computer Protein Binding Ligands Thermodynamics
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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...
Cryoelectron Microscopy Proteins Machine Learning Molecular Dynamics Simulation Protein Conformation
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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 Receptors, Cytoplasmic and Nuclear Thermodynamics Humans Deep Learning Drug Discovery 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...
Signal Transduction Transcription Factors Protein Serine-Threonine Kinases Adaptor Proteins, Signal Transducing DNA-Binding Proteins Molecular Dynamics Simulation Deep Learning Protein Binding Mice Animals TEA Domain Transcription Factors Muscle Proteins Phosphoproteins Hippo Signaling Pathway Trophoblasts YAP-Signaling Proteins Enhancer Elements, Genetic
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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...
Neural Networks, Computer Molecular Dynamics Simulation Software Quantum Theory Graph Neural Networks
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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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