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Molecular Docking Simulation

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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...

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.

SmartCADD: AI-QM Empowered Drug Discovery Platform with Explainability.

Journal of chemical information and modeling
Artificial intelligence (AI) has emerged as a pivotal force in enhancing productivity across various sectors, with its impact being profoundly felt within the pharmaceutical and biotechnology domains. Despite AI's rapid adoption, its integration into...

Chemical analogue based drug design for cancer treatment targeting PI3K: integrating machine learning and molecular modeling.

Molecular diversity
Cancer is a generic term for a group of disorders defined by uncontrolled cell growth and the potential to invade or spread to other parts of the body. Gene and epigenetic alterations disrupt normal cellular control, leading to abnormal cell prolifer...

Integrated structural proteomics and machine learning-guided mapping of a highly protective precision vaccine against mycoplasma pulmonis.

International immunopharmacology
Mycoplasma pulmonis (M. pulmonis) is an emerging respiratory infection commonly linked to prostate cancer, and it is classified under the group of mycoplasmas. Improved management of mycoplasma infections is essential due to the frequent ineffectiven...

Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.

Journal of translational medicine
BACKGROUND: Pancreatic adenocarcinomas (PAADs) often exhibit a "cold" or immunosuppressive tumor milieu, which is associated with resistance to immune checkpoint blockade therapy; however, the underlying mechanisms are incompletely understood. Here, ...