AIMC Topic: Molecular Dynamics Simulation

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Improving Covalent and Noncovalent Molecule Generation via Reinforcement Learning with Functional Fragments.

Journal of chemical information and modeling Jun 5, 2025
Small-molecule drugs play a critical role in cancer therapy by selectively targeting key signaling pathways that drive tumor growth. While deep learning models have advanced drug discovery, there remains a lack of generative frameworks for covalent ...
Agammaglobulinaemia Tyrosine Kinase Small Molecule Libraries ErbB Receptors Protein Kinase Inhibitors Molecular Docking Simulation Drug Design Molecular Dynamics Simulation Ligands Deep Learning Humans
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Machine learning framework coupled with CADD for predicting sphingosine kinase 1 inhibitors.

Computers in biology and medicine Jun 4, 2025
Sphingosine kinase 1 (SphK1) plays a pivotal role in cancer progression, metastasis, and chemotherapy resistance, making it a key target for therapeutic interventions in cancer, cardiovascular diseases, and inflammation. Machine learning models, incl...
Humans Support Vector Machine Molecular Dynamics Simulation Enzyme Inhibitors Machine Learning Molecular Docking Simulation Protein Kinase Inhibitors Phosphotransferases (Alcohol Group Acceptor)
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Comparing models and experimental structures of the GPR101 receptor: Artificial intelligence yields highly accurate models.

Journal of molecular graphics & modelling Jun 3, 2025
Experimental structures solved through cryo-electron microscopy have recently been published for GPR101, a G protein-coupled receptor (GPCR) implicated in the genetic condition X-linked acrogigantism (X-LAG). Here, we compared these experimental stru...
Humans Artificial Intelligence Protein Binding Amino Acid Sequence Protein Conformation Cryoelectron Microscopy Models, Molecular Receptors, G-Protein-Coupled Molecular Dynamics Simulation
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Disruption of Hsp70.14-BAG2 Protein-Protein interactions using deep Learning-Driven peptide design and molecular simulations.

Computers in biology and medicine Jun 3, 2025
Protein-protein interactions (PPIS) are critical in proteostasis, stress response, and disease progression. Targeting the interaction between Hsp70.14 and BAG2, a co-chaperone implicated in oncogenic survival, offers a promising therapeutic approach....
Mitochondrial Proteins Protein Binding Chaperonin 60 Molecular Dynamics Simulation Humans Molecular Docking Simulation HSP70 Heat-Shock Proteins Molecular Chaperones Deep Learning Antimicrobial Peptides
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Melting Profile of DNA in Crowded Solution: Model-Based Study.

International journal of molecular sciences May 31, 2025
Recent advances in molecular dynamics (MD) simulations and the introduction of artificial intelligence (AI) have resulted in a significant increase in accuracy for structure prediction. However, the cell is a highly crowded environment consisting of ...
Nucleic Acid Denaturation Nucleic Acid Conformation DNA Molecular Dynamics Simulation Solutions
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Exploration of the potential therapeutic effects and targets of Coriandrum sativum on non-erosive esophagitis based on bioinformatics and molecular dynamics simulation.

Scientific reports May 31, 2025
Gastroesophageal reflux disease (GERD) is one of the most frequently diagnosed gastrointestinal disorders, adversely affecting quality of life. Coriandrum sativum has been shown to effectively promote gastrointestinal motility, alleviate gastric disc...
Esophagitis Humans Coriandrum Molecular Docking Simulation Molecular Dynamics Simulation Gastroesophageal Reflux Gene Regulatory Networks Protein Interaction Maps Computational Biology
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Molecular insights into the unique activation and allosteric modulation mechanisms of the human mas-related G-protein-coupled receptor X1.

International journal of biological macromolecules May 30, 2025
MRGPRX1 plays dual roles in mediating nociception and pruritus, making it a promising target for alleviating itch and inhibiting pain. However, the mechanisms underlying MRGPRX1 activation and allosteric modulation remain poorly understood, posing si...
Binding Sites Allosteric Regulation Molecular Dynamics Simulation Protein Binding Protein Conformation Receptors, Neuropeptide Receptors, G-Protein-Coupled Humans
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AI, docking, and molecular dynamics to track the binding of structural peptides to different keratin models.

International journal of biological macromolecules May 30, 2025
The present work shows a computational approach to assess the interactions of different nature-inspired peptides with hair keratin models. An updated keratin model was validated, and comparisons with previous models were traced, thereby highlighting ...
Peptides Molecular Docking Simulation Molecular Dynamics Simulation Amino Acid Sequence Protein Binding Artificial Intelligence Keratins
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In Silico Screening of Small Molecule Inhibitors for Amyloid-β Aggregation.

Journal of chemical information and modeling May 29, 2025
The self-aggregation of amyloid-β (Aβ) into fibrils is a hallmark of Alzheimer's disease (AD). Inhibition of Aβ aggregation with small molecule compounds represents a promising therapeutic strategy for AD. However, designing effective ligands is chal...
Machine Learning Molecular Docking Simulation Drug Evaluation, Preclinical Small Molecule Libraries Humans Amyloid beta-Peptides Ligands Molecular Dynamics Simulation Protein Aggregates
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Substrate Activation Efficiency in Active Sites of Hydrolases Determined by QM/MM Molecular Dynamics and Neural Networks.

International journal of molecular sciences May 26, 2025
The active sites of enzymes are able to activate substrates and perform chemical reactions that cannot occur in solutions. We focus on the hydrolysis reactions catalyzed by enzymes and initiated by the nucleophilic attack of the substrate's carbonyl ...
Hydrolases Quantum Theory Neural Networks, Computer Hydrolysis Substrate Specificity Molecular Dynamics Simulation Catalytic Domain
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