AIMC Topic: Molecular Dynamics Simulation

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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 ...
Protease Inhibitors Coronavirus 3C Proteases Molecular Dynamics Simulation Catalytic Domain Middle East Respiratory Syndrome Coronavirus Molecular Docking Simulation Drug Discovery Humans Antiviral Agents Machine Learning
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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 ...
Phosphorylation Molecular Dynamics Simulation Protein Conformation Humans Deep Learning Protein Binding Protein Kinase Inhibitors Thermodynamics Cyclin-Dependent Kinase 6
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Mechanistic Study of Protein Interaction with Natto Inhibitory Peptides Targeting Xanthine Oxidase: Insights from Machine Learning and Molecular Dynamics Simulations.

Journal of chemical information and modeling Mar 24, 2025
Bioactive peptides from food sources offer a safe and biocompatible approach to enzyme inhibition, with potential applications in managing metabolic disorders such as hyperuricemia and gout, conditions linked to excessive xanthine oxidase activity. U...
Machine Learning Peptides Protein Binding Bacillus subtilis Xanthine Oxidase Humans Molecular Dynamics Simulation Enzyme Inhibitors
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Pan-cancer analysis of CDC7 in human tumors: Integrative multi-omics insights and discovery of novel marine-based inhibitors through machine learning and computational approaches.

Computers in biology and medicine Mar 22, 2025
Cancer remains a significant global health challenge, with the Cell Division Cycle 7 (CDC7) protein emerging as a potential therapeutic target due to its critical role in tumor proliferation, survival, and resistance. However, a comprehensive analysi...
Cell Cycle Proteins Drug Discovery Multiomics Biomarkers, Tumor Humans Antineoplastic Agents Protein Serine-Threonine Kinases Neoplasms Machine Learning Molecular Docking Simulation Molecular Dynamics Simulation Computational Biology
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Binding mechanism of inhibitors to DFG-in and DFG-out P38α deciphered using multiple independent Gaussian accelerated molecular dynamics simulations and deep learning.

SAR and QSAR in environmental research Mar 20, 2025
P38α has been identified as a key target for drug design to treat a wide range of diseases. In this study, multiple independent Gaussian accelerated molecular dynamics (GaMD) simulations, deep learning (DL), and the molecular mechanics generalized Bo...
Protein Binding Molecular Dynamics Simulation Quantitative Structure-Activity Relationship Drug Design Deep Learning Mitogen-Activated Protein Kinase 14
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Deciphering the Pharmacological Potential of Kouqiangjie Formula for the Treatment of Diabetic Periodontitis Based on Network Pharmacology, Machine Learning, Molecular Dynamics, and Animal Experiments.

Drug design, development and therapy Mar 20, 2025
BACKGROUND: Periodontitis (PD) and type 2 diabetes mellitus (T2DM) represent interlinked global health burdens, commonly causing significant clinical complications when coincident. Therefore, managing both conditions (T2DM with periodontitis, DP) sim...
Network Pharmacology Rats Rats, Sprague-Dawley Male Periodontitis Machine Learning Molecular Docking Simulation Drugs, Chinese Herbal Animals Diabetes Mellitus, Type 2 Diabetes Mellitus, Experimental Molecular Dynamics Simulation
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Integrated AI and machine learning pipeline identifies novel WEE1 kinase inhibitors for targeted cancer therapy.

Molecular diversity Mar 19, 2025
The dysregulation of the cell cycle in cancer underscores the therapeutic potential of targeting WEE1 kinase, a key regulator of the G2/M checkpoint. This study harnessed artificial intelligence (AI)-driven methodologies, particularly the MORLD platf...
Protein Kinase Inhibitors Cell Cycle Proteins Neoplasms Molecular Docking Simulation Humans Antineoplastic Agents Artificial Intelligence Protein-Tyrosine Kinases Machine Learning Molecular Dynamics Simulation Molecular Targeted Therapy
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Unsupervised Learning of Progress Coordinates during Weighted Ensemble Simulations: Application to NTL9 Protein Folding.

Journal of chemical theory and computation Mar 19, 2025
A major challenge for many rare-event sampling strategies is the identification of progress coordinates that capture the slowest relevant motions. Machine-learning methods that can identify progress coordinates in an unsupervised manner have therefor...
Molecular Dynamics Simulation Markov Chains Protein Folding Deep Learning Unsupervised Machine Learning
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Probing the dark chemical matter against PDE4 for the management of psoriasis using in silico, in vitro and in vivo approach.

Molecular diversity Mar 17, 2025
The potential downsides for the present treatment for psoriasis are drug resistance, reduced efficacy, risk of mental episodes, and drug interactions. Hence, this study aims to discover a new drug for psoriasis by considering global research efforts ...
Animals Molecular Docking Simulation Drug Discovery Ligands Mice Humans Psoriasis Phosphodiesterase 4 Inhibitors Molecular Dynamics Simulation Cyclic Nucleotide Phosphodiesterases, Type 4
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Computational discovery of novel PI3KC2α inhibitors using structure-based pharmacophore modeling, machine learning and molecular dynamic simulation.

Journal of molecular graphics & modelling Mar 15, 2025
PI3KC2α is a lipid kinase associated with cancer metastasis and thrombosis. In this study, we present a novel computational workflow integrating structure-based pharmacophore modeling, machine learning (ML), and molecular dynamics (MD) simulations to...
Pharmacophore Protein Binding Phosphatidylinositol 3-Kinases Molecular Dynamics Simulation Machine Learning Ligands Molecular Docking Simulation Protein Kinase Inhibitors Humans Drug Discovery Phosphoinositide-3 Kinase Inhibitors
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