AIMC Topic: Molecular Dynamics Simulation
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Utilizing machine learning and molecular dynamics for enhanced drug delivery in nanoparticle systems.
Scientific reports
Nov 4, 2024
Materials data science and machine learning (ML) are pivotal in advancing cancer treatment strategies beyond traditional methods like chemotherapy. Nanotherapeutics, which merge nanotechnology with targeted drug delivery, exemplify this advancement b...
Machine-Learning Approach to Identify Potential Dengue Virus Protease Inhibitors: A Computational Perspective.
The journal of physical chemistry. B
Nov 1, 2024
The global prevalence of dengue virus (DENV), a widespread flavivirus, has led to varied epidemiological impacts, economic burdens, and health consequences. The alarming increase in infections is exacerbated by the absence of approved antiviral agent...
A Bio-Inspired Magnetic Soft Robotic Fish for Efficient Solar-Energy Driven Water Purification.
Small methods
Oct 24, 2024
Solar-driven water evaporation is a promising solution for global water scarcity but is still facing challenges due to its substantial energy requirements. Here, a magnetic soft robotic bionic fish is developed by combining magnetic nanoparticles (Fe...
Pre-training strategy for antiviral drug screening with low-data graph neural network: A case study in HIV-1 K103N reverse transcriptase.
Journal of computational chemistry
Oct 22, 2024
Graph neural networks (GNN) offer an alternative approach to boost the screening effectiveness in drug discovery. However, their efficacy is often hindered by limited datasets. To address this limitation, we introduced a robust GNN training framework...
Tackling APOE's structural challenges via in silico modeling in the era of neural networks: Can AlphaFold II help circumvent the problem of lacking full-length protein structure?
Archives of biochemistry and biophysics
Oct 22, 2024
The APOE gene, encoding apolipoprotein E, is a predictor of longevity and age-related diseases. Despite numerous genetic studies, the data on molecular mechanisms by which apolipoprotein E affects the human phenotype remain incomplete due to the stru...
Machine learning models to identify lead compound and substitution optimization to have derived energetics and conformational stability through docking and MD simulations for sphingosine kinase 1.
Molecular diversity
Oct 17, 2024
Sphingosine kinases (SphKs) are a group of important enzymes that circulate at low micromolar concentrations in mammals and have received considerable attention due to the roles they play in a broad array of biological processes including apoptosis, ...
Towards novel small-molecule inhibitors blocking PD-1/PD-L1 pathway: From explainable machine learning models to molecular dynamics simulation.
International journal of biological macromolecules
Oct 15, 2024
Molecular design of small-molecule inhibitors targeting programmed cell death-1 (PD-1)/programmed cell death ligand-1 (PD-L1) pathway has been recognized as an active research area by the clinical success of cancer immunotherapy. In recent years, usi...
High-throughput and computational techniques for aptamer design.
Expert opinion on drug discovery
Oct 10, 2024
INTRODUCTION: Aptamers refer to short ssDNA/RNA sequences that target small molecules, proteins, or cells. Aptamers have significantly advanced diagnostic applications, including biosensors for detecting specific biomarkers, state-of-the-art imaging,...
Exploring Protein Conformational Changes Using a Large-Scale Biophysical Sampling Augmented Deep Learning Strategy.
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Oct 10, 2024
Inspired by the success of deep learning in predicting static protein structures, researchers are now actively exploring other deep learning algorithms aimed at predicting the conformational changes of proteins. Currently, a major challenge in the de...
Deciphering Cathepsin K inhibitors: a combined QSAR, docking and MD simulation based machine learning approaches for drug design.
SAR and QSAR in environmental research
Oct 9, 2024
Cathepsin K (CatK), a lysosomal cysteine protease, contributes to skeletal abnormalities, heart diseases, lung inflammation, and central nervous system and immune disorders. Currently, CatK inhibitors are associated with severe adverse effects, there...
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