AIMC Topic: Molecular Docking Simulation

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AI-driven protein pocket detection through integrating deep Q-networks for structural analysis.

Journal of computer-aided molecular design
Protein pockets, or small cavities on the protein surface, are critical sites for enzymatic catalysis, molecular recognition, and drug binding. Accurately identifying these pockets is crucial for understanding protein function and designing therapeut...

Developing a predictive QSAR model for FGFR-1 inhibitors: integrating computational and experimental validation.

Journal of computer-aided molecular design
The traditional drug discovery process is often lengthy, costly, and characterized by a high failure rate. There is a pressing need for innovative strategies to optimize this process and improve the chances of identifying effective therapeutic candid...

GENEOnet: a breakthrough in protein binding pocket detection using group equivariant non-expansive operators.

Scientific reports
Structure-based virtual screening approaches like molecular docking rely on accurately identifying and precisely calculating binding pockets to efficiently search for potential ligands. In this paper, we introduce GENEOnet, a machine learning model d...

Discovering of novel umami-enhancing peptides from Flammulina filiformis: Combining virtual screening, machine learning, molecular dynamics simulations, and sensory evaluation.

Food chemistry
This research employed integrated machine learning and bioinformatics approaches to identify umami-enhancing peptides from Flammulina filiformis, elucidate their mechanisms of umami augmentation, and validate their efficacy through sensory evaluation...

Identification of a novel Aurora B inhibitor using the AI-driven drug screening and docking-based traditional screening.

Bioorganic & medicinal chemistry
Aurora B, a subtype of Aurora kinases that functions as a serine/threonine kinase, playing a vital role in the process of mitosis, is often overexpressed in certain tumor cells leading to tumorigenesis and progression. Therefore, the development of s...

CNSGT: Generative Transformer for De Novo Drug Design Targeting the Central Nervous System.

Journal of chemical information and modeling
The design of novel central nervous system (CNS) drugs presents formidable challenges due to the restrictive nature of the blood-brain barrier, which imposes stringent physicochemical requirements. Recent advances in deep learning, particularly Trans...

Design, Synthesis, and Aphicidal Activity of Novel Insect Neuropeptide Kinin Receptor Antagonists, Targeting the Ser Ligand Position.

Journal of agricultural and food chemistry
Traditional chemical pesticides have raised significant environmental and health concerns, driving the pursuit of safer alternatives. Aphids, notorious for causing extensive agricultural damage and transmitting plant diseases, represent prime targets...

Integrated Machine Learning and Structure-Based Virtual Screening Identify Osimertinib as a TNIK Inhibitor for Idiopathic Pulmonary Fibrosis.

Journal of chemical information and modeling
Traf2-and Nck-interacting kinase (TNIK) has been implicated in fibrosis-associated signaling pathways and has recently emerged as a promising therapeutic target for idiopathic pulmonary fibrosis (IPF). In this study, we employed an integrated strateg...

Identification of genes related to the effects of bicalutamide and zoladex on benign prostatic hyperplasia.

Scientific reports
Existing research indicates that bicalutamide and zoladex show significant potential in treating prostate cancer. However, in the clinical application of treating benign prostatic hyperplasia (BPH), it is limited due to relatively severe side effects...

Investigate the potential inhibitors of sphingosine kinase 1 (SphK1) with molecular dynamics and artificial intelligence drug design methods.

Journal of molecular modeling
CONTEXT: Sphingosine kinase 1 (SphK1) is a sphingosine kinase that can catalyze the phosphorylation of sphingosine to generate sphingosine-1-phosphate. The J-type channel of SPHK1 plays an important role in processes such as cell signaling. Therefore...