AIMC Topic: Molecular Dynamics Simulation
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Engineered multi-domain lipid nanoparticles for targeted delivery.
Chemical Society reviews
Jun 16, 2025
Engineered lipid nanoparticles (LNPs) represent a breakthrough in targeted drug delivery, enabling precise spatiotemporal control essential to treat complex diseases such as cancer and genetic disorders. However, the complexity of the delivery proces...
Enzymatic carbon-fluorine bond cleavage by human gut microbes.
Proceedings of the National Academy of Sciences of the United States of America
Jun 13, 2025
Fluorinated compounds are used for agrochemical, pharmaceutical, and numerous industrial applications, resulting in global contamination. In many molecules, fluorine is incorporated to enhance the half-life and improve bioavailability. Fluorinated co...
Smart Reaction Templating: A Graph-Based Method for Automated Molecular Dynamics Input Generation.
Journal of chemical information and modeling
Jun 6, 2025
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and postreaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that automates the gener...
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 ...
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...
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....
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 ...
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...
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...
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 ...
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