AIMC Topic: Molecular Docking Simulation

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Leveraging new approach methodologies: ecotoxicological modelling of endocrine disrupting chemicals to Danio rerio through machine learning and toxicity studies.

Toxicology mechanisms and methods
New approach methodologies (NAMs) offer information tailored to the intended application while reducing the use of animals. NAMs aim to develop quantitative structure-activity relationship (QSAR) and quantitive-Read-Across structure-activity relation...

In silico assessments of the small molecular boron agents to pave the way for artificial intelligence-based boron neutron capture therapy.

European journal of medicinal chemistry
Boron neutron capture therapy (BNCT) is a highly targeted, selective and effective technique to cure various types of cancers, with less harm to the healthy cells. In principle, BNCT treatment needs to distribute the boron (B) atoms inside the tumor ...

Investigating PCB degradation by indigenous fungal strains isolated from the transformer oil-contaminated site: degradation kinetics, Bayesian network, artificial neural networks, QSAR with DFT, molecular docking, and molecular dynamics simulation.

Environmental science and pollution research international
The widespread prevalence of polychlorinated biphenyls (PCBs) in the environment has raised major concerns due to the associated risks to human health, wildlife, and ecological systems. Here, we investigated the degradation kinetics, Bayesian network...

Combining network pharmacology, machine learning, molecular docking and molecular dynamic to explore the mechanism of Chufeng Qingpi decoction in treating schistosomiasis.

Frontiers in cellular and infection microbiology
BACKGROUND: Although the Chufeng Qingpi Decoction (CQD) has demonstrated clinical effectiveness in the treatment of schistosomiasis, the precise active components and the underlying mechanisms of its therapeutic action remain elusive. To achieve a pr...

Teaching old docks new tricks with machine learning enhanced ensemble docking.

Scientific reports
We here introduce Ensemble Optimizer (EnOpt), a machine-learning tool to improve the accuracy and interpretability of ensemble virtual screening (VS). Ensemble VS is an established method for predicting protein/small-molecule (ligand) binding. Unlike...

An artificial intelligence accelerated virtual screening platform for drug discovery.

Nature communications
Structure-based virtual screening is a key tool in early drug discovery, with growing interest in the screening of multi-billion chemical compound libraries. However, the success of virtual screening crucially depends on the accuracy of the binding p...

Machine learning, network pharmacology, and molecular dynamics reveal potent cyclopeptide inhibitors against dengue virus proteins.

Molecular diversity
The dengue virus is a major global health hazard responsible for an estimated 390 million diseases yearly. This study focused on identifying cyclopeptide inhibitors for envelope structural proteins E, NS1, NS3, and NS5. Additionally, 5579 cyclopeptid...

Innovative virtual screening of PD-L1 inhibitors: the synergy of molecular similarity, neural networks and GNINA docking.

Future medicinal chemistry
Immune checkpoint inhibitors targeting PD-L1 are crucial in cancer research for preventing cancer cells from evading the immune system. This study developed a screening model combining ANN, molecular similarity, and GNINA 1.0 docking to target PD-L1...

Identification of cancer stem cell-related genes through single cells and machine learning for predicting prostate cancer prognosis and immunotherapy.

Frontiers in immunology
BACKGROUND: Cancer stem cells (CSCs) are a subset of cells within tumors that possess the unique ability to self-renew and give rise to diverse tumor cells. These cells are crucial in driving tumor metastasis, recurrence, and resistance to treatment....

Identification of key immune-related genes and potential therapeutic drugs in diabetic nephropathy based on machine learning algorithms.

BMC medical genomics
BACKGROUND: Diabetic nephropathy (DN) is a major contributor to chronic kidney disease. This study aims to identify immune biomarkers and potential therapeutic drugs in DN.