AIMC Topic: Molecular Dynamics Simulation

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Characterization of binding kinetics and intracellular signaling of new psychoactive substances targeting cannabinoid receptor using transition-based reweighting method.

eLife
New psychoactive substances (NPS) targeting human cannabinoid receptor 1 pose a significant threat to society as recreational abusive drugs that have pronounced physiological side effects. These greater adverse effects compared to classical cannabino...

Study on the Adsorption Performance of Ionic Liquids Based on Molecular Dynamics and Interpretable Machine Learning.

Journal of chemical information and modeling
The stable adsorption behavior of ionic liquid lubricants at metal interfaces is a key mechanism for achieving their excellent friction-reducing and antiwear properties. This study employs a research strategy that combines high-throughput molecular d...

IR Spectroscopy: From Experimental Spectra to High-Resolution Structural Analysis by Integrating Simulations and Machine Learning.

The journal of physical chemistry. B
Understanding biomolecular function at the atomic scale requires detailed insight into the structural changes underlying dynamic processes. Vibrational infrared (IR) spectroscopy─when paired with biomolecular simulations and quantum-chemical calculat...

In silico Techniques for the Investigation of Bioactive Compounds in Quinoa (Chenopodium quinoa Willd.): Recent Advances in Molecular Modeling and Identification of Therapeutic Targets.

Plant foods for human nutrition (Dordrecht, Netherlands)
Quinoa (Chenopodium quinoa Willd.) is a valuable source of bioactive compounds with therapeutic potential, including peptides, saponins, and polyphenols. In recent years, in silico tools have emerged as key strategies for predicting, characterizing, ...

Identification of hub necroptosis-related targets and discovery of potential natural inhibitors in ulcerative colitis based on bioinformatics and computer-aided drug design.

Journal of computer-aided molecular design
Ulcerative colitis (UC) is a chronic inflammatory bowel disease with a complex pathogenesis and limited treatment options. Recently, necroptosis has been found to play a significant role in UC. This study aimed to investigate necroptosis-related mech...

Integrated experimental, computational and machine learning approaches for the development of Apremilast-Aceclofenac coamorphous systems.

International journal of pharmaceutics
Understanding the molecular mechanisms of drug coamorphization remains a key challenge in solid-state pharmaceutics. This study presents a molecular level strategy for designing drug-drug coamorphous systems (CAMs) of apremilast (APR) and aceclofenac...

Probing the Gate-Opening Transition in the Bacterial ClpP Peptidase Using Molecular Dynamics Simulations and Machine Learning.

Biochemistry
Preserving proteome integrity is crucial for maintaining cell viability across all kingdoms of life. The bacterial caseinolytic protease (ClpP) plays a critical role in maintaining protein homeostasis by degrading misfolded or damaged proteins within...

AI-Guided Hydrophobic Core Design of Robust Six-Helix Bundle Proteins.

ACS nano
α-Helical domains are widespread and versatile, yet typically fail under low mechanical load because backbone hydrogen bonds unzip sequentially, limiting their use in force-bearing nanomaterials and molecular devices. We present an AI-guided strategy...

Predicting the Impact of Drug Resistance Mutations on Inhibitor Potency with Molecular Dynamics and Machine Learning.

The journal of physical chemistry. B
Many enzymes are vital drug targets in diseases such as cancer and pathogenic infections; however, mutations can drastically disrupt inhibitor binding to confer resistance. Resistance mutations primarily occur at the inhibitor binding site, but accom...

Identification of novel DYRK1A inhibitors as treatment options for alzheimer's disease through comprehensive in silico approaches.

Scientific reports
This study aims to identify potential DYRK1A inhibitors from a curated database and utilize a QSAR model to predict the bioactivity of drug compounds in inhibiting the enzyme involved in tau protein oligomerization, a key process in AD pathology. 192...