AIMC Topic: Molecular Dynamics Simulation

Clear Filters Showing 41 to 50 of 545 articles

In silico discovery of novel compounds for FAK activation using virtual screening, AI-based prediction, and molecular dynamics.

Computational biology and chemistry Mar 25, 2025
Focal Adhesion Kinase (FAK) is a non-receptor tyrosine kinase that plays a crucial role in cell proliferation, migration, and signal transduction. FAK is overexpressed in metastatic and advanced-stage cancers, where it is considered a key kinase in c...
Drug Evaluation, Preclinical Protein Kinase Inhibitors Focal Adhesion Protein-Tyrosine Kinases Molecular Structure Molecular Dynamics Simulation Artificial Intelligence Molecular Docking Simulation Drug Discovery Humans
View on PubMed DOI

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...
Humans Machine Learning Peptides Protein Binding Bacillus subtilis Molecular Dynamics Simulation Enzyme Inhibitors Xanthine Oxidase
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...
Cell Cycle Proteins Protein Serine-Threonine Kinases Humans Antineoplastic Agents Neoplasms Molecular Dynamics Simulation Computational Biology Machine Learning Molecular Docking Simulation Multiomics Biomarkers, Tumor Drug Discovery
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 Quantitative Structure-Activity Relationship Molecular Dynamics Simulation Drug Design 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 Molecular Docking Simulation Drugs, Chinese Herbal Machine Learning Diabetes Mellitus, Type 2 Periodontitis Diabetes Mellitus, Experimental Animals Molecular Dynamics Simulation
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 Molecular Dynamics Simulation Markov Chains Protein Folding
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...
Pharmacophore Protein Kinase Inhibitors Phosphoinositide-3 Kinase Inhibitors Molecular Docking Simulation Phosphatidylinositol 3-Kinases Molecular Dynamics Simulation Ligands Drug Discovery Protein Binding Humans Machine Learning
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...
Deep Learning Aluminum Particle Size Nanostructures Alloys Density Functional Theory Molecular Dynamics Simulation
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...
Malate Dehydrogenase Deep Learning Temperature Evolution, Molecular Enzyme Stability Molecular Dynamics Simulation Protein Conformation Cytosol
View on PubMed DOI

Leveraging AlphaFold models to predict androgenic effects of endocrine-disrupting chemicals through zebrafish androgen receptor analysis.

Toxicology mechanisms and methods Mar 12, 2025
The androgen receptor (AR) activation by androgens is vital for tissue development, sexual differentiation, and reproductive attributes in zebrafish (). However, our understanding of the molecular mechanisms behind their activation remains limited. I...
Testosterone Molecular Dynamics Simulation Zebrafish Animals Molecular Docking Simulation Endocrine Disruptors Ligands Androgens Zebrafish Proteins Dihydrotestosterone Receptors, Androgen
View on PubMed DOI
Popular Topics
Recent Journals