AIMC Topic: Molecular Dynamics Simulation
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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...
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 ...
In-silico evaluation of Azadirachta indica-derived Daucosterol against key viral proteins of Ebolavirus using ML and MD simulations approach.
Journal of biological physics
May 26, 2025
Ebola virus disease (EVD) is an acute life-threatening disease caused by highly pathogenic Ebolavirus (EBOV), with reported case fatality rates reaching 90%. There have been numerous EBOV outbreaks and epidemics since the first outbreak was reported ...
Novel Antimicrobials from Computational Modelling and Drug Repositioning: Potential Strategies to Increase Therapeutic Arsenal Against Antimicrobial Resistance.
Molecules (Basel, Switzerland)
May 24, 2025
Antimicrobial resistance (AMR) is one of the most significant public health threats today. The need for new antimicrobials against multidrug-resistant infections is growing. The development of computational models capable of predicting new drug-targe...
CrypToth: Cryptic Pocket Detection through Mixed-Solvent Molecular Dynamics Simulations-Based Topological Data Analysis.
Journal of chemical information and modeling
May 22, 2025
Some functional proteins undergo conformational changes to expose hidden binding sites when a binding molecule approaches their surface. Such binding sites are called cryptic sites and are important targets for drug discovery. However, it is still di...
Evolutionary Dynamics and Functional Differences in Clinically Relevant Pen β-Lactamases from spp.
Journal of chemical information and modeling
May 2, 2025
Antimicrobial resistance (AMR) is a global threat, with species contributing significantly to difficult-to-treat infections. The Pen family of β-lactamases are produced by all spp., and their mutation or overproduction leads to the resistance of β-...
Predicting biomolecule adsorption on nanomaterials: a hybrid framework of molecular simulations and machine learning.
Nanoscale
May 2, 2025
The adsorption of biomolecules on the surface of nanomaterials (NMs) is a critical determinant of their behavior, toxicity, and efficacy in biological systems. Experimental testing of these phenomena is often costly or complicated. Computational appr...
Dual-Site Targeting by Peptide Inhibitors of the N-Terminal Domain of Hsp90: Mechanism and Design.
Journal of chemical information and modeling
May 1, 2025
Heat shock protein 90 (Hsp90) is a pivotal molecular chaperone crucial in the maturation of client proteins, positioning it as a significant target for cancer therapy. However, the design of effective Hsp90 inhibitors presents substantial challenges ...
Dynamics and Machine Learning Reveal the Link between Tripeptide Sequences and Evaporation-Driven Material Properties.
Nano letters
Apr 27, 2025
Previous research showed that a peptide composed of three tyrosines (YYY) can turn into organic glass and cause strong adhesion between substrates via evaporation. However, the mechanisms of these processes remain unclear, and the exploration of appl...
Multiscale insights into cornuside's effects on NAFLD: A cross-disciplinary integrating bioinformatics, computational chemistry, and machine learning.
Phytomedicine : international journal of phytotherapy and phytopharmacology
Apr 26, 2025
BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is a complex metabolic disorder involving intertwined signaling pathways, posing challenges for targeted therapeutic interventions. Cornus Fructus (CF), a traditional medicinal herb, holds potenti...
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