AIMC Topic: Molecular Docking Simulation

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

Journal of chemical information and modeling
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 ...

Targeting INF2 with DiosMetin 7-O-β-D-Glucuronide: a new stratagem for colorectal cancer therapy.

BMC cancer
BACKGROUND AND PURPOSE: Colorectal cancer (CRC) is the third most prevalent malignancy in the gastrointestinal tract and the second leading cause of cancer-related deaths. Despite the identification of numerous biomarkers, their non-specific distribu...

Exploration of the potential therapeutic effects and targets of Coriandrum sativum on non-erosive esophagitis based on bioinformatics and molecular dynamics simulation.

Scientific reports
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...

AI, docking, and molecular dynamics to track the binding of structural peptides to different keratin models.

International journal of biological macromolecules
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 ...

Integrated bioinformatics and network pharmacology to identify and validate macrophage polarization related hub genes in the treatment of osteoarthritis with Astragalus membranaceus.

Journal of orthopaedic surgery and research
BACKGROUND: Macrophage polarization exacerbates the pathological processes of osteoarthritis (OA). Astragalus membranaceus (AM) can repair chondrocytes and serve as a protective agent for OA. Therefore, the study intended to identify macrophage polar...

In Silico Screening of Small Molecule Inhibitors for Amyloid-β Aggregation.

Journal of chemical information and modeling
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...

Molecular mechanisms of deer antler in promoting osteogenic differentiation of human mesenchymal stem cells via JUN modulation.

Frontiers in immunology
BACKGROUND: Traditional Chinese medicine and food deer antler has been extensively used in bone regeneration, but its molecular mechanisms remain poorly understood. Preliminary investigations suggest deer antler contains bioactive compounds that infl...

Reliable protein-protein docking with AlphaFold, Rosetta, and replica exchange.

eLife
Despite the recent breakthrough of AlphaFold (AF) in the field of protein sequence-to-structure prediction, modeling protein interfaces and predicting protein complex structures remains challenging, especially when there is a significant conformation...

In-silico evaluation of Azadirachta indica-derived Daucosterol against key viral proteins of Ebolavirus using ML and MD simulations approach.

Journal of biological physics
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 ...