AIMC Topic: Molecular Dynamics Simulation

Clear Filters Showing 71 to 80 of 597 articles

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...
Enzyme Inhibitors Machine Learning Xanthine Oxidase Peptides Bacillus subtilis Molecular Dynamics Simulation Protein Binding Humans
View on PubMed DOI

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...
Machine Learning Biomarkers, Tumor Neoplasms Molecular Docking Simulation Drug Discovery Antineoplastic Agents Humans Molecular Dynamics Simulation Cell Cycle Proteins Computational Biology Multiomics Protein Serine-Threonine Kinases
View on PubMed DOI

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...
Deep Learning Protein Binding Molecular Dynamics Simulation Drug Design Quantitative Structure-Activity Relationship Mitogen-Activated Protein Kinase 14
View on PubMed DOI

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 Male Rats, Sprague-Dawley Drugs, Chinese Herbal Molecular Docking Simulation Machine Learning Periodontitis Diabetes Mellitus, Experimental Animals Molecular Dynamics Simulation Diabetes Mellitus, Type 2
View on PubMed DOI

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
View on PubMed DOI

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...
Deep Learning Unsupervised Machine Learning Protein Folding Molecular Dynamics Simulation Markov Chains
View on PubMed DOI

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 Humans Ligands Phosphodiesterase 4 Inhibitors Mice Cyclic Nucleotide Phosphodiesterases, Type 4 Psoriasis Molecular Dynamics Simulation
View on PubMed DOI

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...
Phosphoinositide-3 Kinase Inhibitors Pharmacophore Ligands Protein Kinase Inhibitors Machine Learning Molecular Docking Simulation Drug Discovery Protein Binding Phosphatidylinositol 3-Kinases Molecular Dynamics Simulation Humans
View on PubMed DOI

Deep-Learning Potential Molecular Dynamics Study on Nanopolycrystalline Al-Er Alloys: Effects of Er Concentration, Grain Boundary Segregation, and Grain Size on Plastic Deformation.

Journal of chemical information and modeling Mar 14, 2025
Understanding the tensile mechanical properties of Al-Er alloys at the atomic scale is essential, and molecular dynamics (MD) simulations offer valuable insights. However, these simulations are constrained by the unavailability of suitable interatomi...
Molecular Dynamics Simulation Nanostructures Alloys Particle Size Density Functional Theory Deep Learning Aluminum
View on PubMed DOI

Thermal Adaptation of Cytosolic Malate Dehydrogenase Revealed by Deep Learning and Coevolutionary Analysis.

Journal of chemical theory and computation Mar 13, 2025
Protein evolution has shaped enzymes that maintain stability and function across diverse thermal environments. While sequence variation, thermal stability and conformational dynamics are known to influence an enzyme's thermal adaptation, how these fa...
Molecular Dynamics Simulation Enzyme Stability Protein Conformation Temperature Deep Learning Evolution, Molecular Cytosol Malate Dehydrogenase
View on PubMed DOI
Popular Topics
Recent Journals