AIMC Topic: Molecular Dynamics Simulation

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Evaluation of Machine Learning/Molecular Mechanics End-State Corrections with Mechanical Embedding to Calculate Relative Protein-Ligand Binding Free Energies.

Journal of chemical theory and computation Jan 3, 2025
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are several ti...
Machine Learning Protein Binding Quantum Theory Ligands Thermodynamics Proteins Molecular Dynamics Simulation
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Unveiling key drivers of hepatocellular carcinoma: a synergistic approach with network pharmacology, machine learning-driven ligand discovery and dynamic simulations.

SAR and QSAR in environmental research Jan 3, 2025
Hepatocellular carcinoma (HCC) ranks fourth in cancer-related mortality worldwide. This study aims to uncover the genes and pathways involved in HCC through network pharmacology (NP) and to discover potential drugs via machine learning (ML)-based lig...
Glycogen Synthase Kinase 3 beta Network Pharmacology Carcinoma, Hepatocellular Proto-Oncogene Proteins c-akt Molecular Docking Simulation Molecular Dynamics Simulation Humans Drug Discovery Ligands Machine Learning Liver Neoplasms Quantitative Structure-Activity Relationship
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On the emergence of machine-learning methods in bottom-up coarse-graining.

Current opinion in structural biology Jan 2, 2025
Machine-learning methods have gained significant attention in the computational chemistry community as a viable approach to molecular modeling and analysis. Recent successes in utilizing neural networks to learn atomistic force-fields which 'coarse-g...
Neural Networks, Computer Machine Learning Models, Molecular Molecular Dynamics Simulation Thermodynamics
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In silico design of dehydrophenylalanine containing peptide activators of glucokinase using pharmacophore modelling, molecular dynamics and machine learning: implications in type 2 diabetes.

Journal of computer-aided molecular design Dec 31, 2024
Diabetes represents a significant global health challenge associated with substantial healthcare costs and therapeutic complexities. Current diabetes therapies often entail adverse effects, necessitating the exploration of novel agents. Glucokinase (...
Glucokinase Enzyme Activators Phenylalanine Pharmacophore Peptides Molecular Docking Simulation Drug Design Diabetes Mellitus, Type 2 Hypoglycemic Agents Molecular Dynamics Simulation Humans Machine Learning Computer Simulation
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SchNet_IIA: Potential Energy Surface Fitting by Interatomic Interactions Attention Based on Transfer Learning Analysis.

Journal of chemical information and modeling Dec 30, 2024
Machine learning methods for fitting potential energy surfaces and molecular dynamics simulations are becoming increasingly popular due to their potentially high accuracy and savings in computational resources. However, existing application models of...
Neural Networks, Computer Machine Learning Molecular Dynamics Simulation Surface Properties Thermodynamics
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Harnessing the Power of Machine Learning Guided Discovery of NLRP3 Inhibitors Towards the Effective Treatment of Rheumatoid Arthritis.

Cells Dec 30, 2024
The NLRP3 inflammasome, plays a critical role in the pathogenesis of rheumatoid arthritis (RA) by activating inflammatory cytokines such as IL1β and IL18. Targeting NLRP3 has emerged as a promising therapeutic strategy for RA. In this study, a multid...
Arthritis, Rheumatoid NLR Family, Pyrin Domain-Containing 3 Protein Molecular Dynamics Simulation Chemical Phenomena Antirheumatic Agents Machine Learning Databases, Chemical Quantitative Structure-Activity Relationship
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Study on SHP2 Conformational Transition and Structural Characterization of Its High-Potency Allosteric Inhibitors by Molecular Dynamics Simulations Combined with Machine Learning.

Molecules (Basel, Switzerland) Dec 24, 2024
The src-homology 2 domain-containing phosphatase 2 (SHP2) is a human cytoplasmic protein tyrosine phosphatase that plays a crucial role in cellular signal transduction. Aberrant activation and mutations of SHP2 are associated with tumor growth and im...
Allosteric Regulation Protein Tyrosine Phosphatase, Non-Receptor Type 11 Enzyme Inhibitors Machine Learning Protein Conformation Protein Binding Humans Molecular Dynamics Simulation
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Identification of STAT3 phosphorylation inhibitors using generative deep learning, virtual screening, molecular dynamics simulations, and biological evaluation for non-small cell lung cancer therapy.

Molecular diversity Dec 23, 2024
The development of phosphorylation-suppressing inhibitors targeting Signal Transducer and Activator of Transcription 3 (STAT3) represents a promising therapeutic strategy for non-small cell lung cancer (NSCLC). In this study, a generative model was d...
Deep Learning Cell Line, Tumor Lung Neoplasms Molecular Docking Simulation Antineoplastic Agents Molecular Dynamics Simulation STAT3 Transcription Factor Binding Sites Protein Binding Carcinoma, Non-Small-Cell Lung Phosphorylation Humans
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BioStructNet: Structure-Based Network with Transfer Learning for Predicting Biocatalyst Functions.

Journal of chemical theory and computation Dec 20, 2024
Enzyme-substrate interactions are essential to both biological processes and industrial applications. Advanced machine learning techniques have significantly accelerated biocatalysis research, revolutionizing the prediction of biocatalytic activities...
Enzymes Algorithms Deep Learning Molecular Dynamics Simulation Ligands Biocatalysis Machine Learning
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Advanced Mass-Spectra-Based Machine Learning for Predicting the Toxicity of Traditional Chinese Medicines.

Analytical chemistry Dec 20, 2024
Traditional Chinese medicine (TCM) has been a cornerstone of health care for centuries, valued for its preventive and therapeutic properties. However, recent decades have revealed significant toxicological concerns associated with TCMs due to their c...
Machine Learning Medicine, Chinese Traditional Drugs, Chinese Herbal Humans Quantitative Structure-Activity Relationship Molecular Dynamics Simulation Spectrometry, Mass, Electrospray Ionization Cytochrome P-450 CYP3A
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