AIMC Topic: Molecular Docking Simulation

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Harnessing AlphaFold to reveal hERG channel conformational state secrets.

eLife
To design safe, selective, and effective new therapies, there must be a deep understanding of the structure and function of the drug target. One of the most difficult problems to solve has been the resolution of discrete conformational states of tran...

CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches.

Journal of computer-aided molecular design
Identifying orthosteric binding sites and predicting small molecule affinities remains a key challenge in virtual screening. While blind docking explores the entire protein surface, its precision is hindered by the vast search space. Cavity detection...

Integrating machine learning with in silico studies and Quantum Chemistry: Exploring novel compounds through multiscale screening targeting the CDK2 enzyme.

Computers in biology and medicine
Cyclin-dependent kinase 2 (CDK2) modulates the progression of the cell cycle, and its dysregulation results in unchecked cellular proliferation, establishing it as a pivotal target in oncological therapies. We implemented a comprehensive screening pi...

AI based natural inhibitor targeting RPS20 for colorectal cancer treatment using integrated computational approaches.

Scientific reports
The increasing global incidence of cancer emphasizes the vital role of machine learning algorithms and artificial intelligence (AI) in identifying novel anticancer targets and developing new drugs. Computational approaches can significantly quicken r...

Machine learning-based QSAR and structure-based virtual screening guided discovery of novel mIDH1 inhibitors from natural products.

Journal of computer-aided molecular design
Mutations in isocitrate dehydrogenase 1 (IDH1) have been widely observed in various tumors, such as gliomas and acute myeloid leukemia, and therefore has become one of the current research focal points. Therefore, it is crucial to find inhibitors tha...

A computational study of cardiac glycosides from Vernonia amygdalina as PI3K inhibitors for targeting HER2 positive breast cancer.

Journal of computer-aided molecular design
The PI3K/Akt pathway plays a crucial role in regulating a broad network of proteins involved in the proliferation of HER2-positive breast cancer. The ethyl acetate fraction of Vernonia amygdalina, which contains cardiac glycosides, has been shown to ...

Ultrahigh-Throughput Virtual Screening Strategies against PPI Targets: A Case Study of STAT Inhibitors.

Journal of chemical information and modeling
In recent years, virtual screening of ultralarge (10) libraries of synthetically accessible compounds (uHTVS) became a popular approach in hit identification. With AI-assisted virtual screening workflows, such as Deep Docking, these protocols might b...

Uncovering key markers and therapeutic targets for renal fibrosis in diabetic kidney disease through bulk and single-cell RNA sequencing.

Journal of translational medicine
BACKGROUND: Diabetic kidney disease (DKD) is the major cause of chronic kidney failure, with tubulointerstitial fibrosis playing a crucial role in disease development. Identifying fibrosis-related genes is crucial for improving diagnosis and developi...

Computational Strategies to Enhance Vitamin B Biosynthesis Potential of Microbes.

Current microbiology
Vitamin B is a vital nutrient for the normal functioning of many metabolic processes. It has a characteristic corrinoid ring structure with a cobalt ion. Its complex chemical structure demands 30 enzyme-catalyzed steps for synthesis. Deficiency of th...

Exploring Protein-Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches.

Journal of chemical information and modeling
Protein-protein interactions are crucial for numerous biological activities such as signaling, enzyme catalysis, gene expression regulation, cell adhesion, immune response, and drug action. Structural characterization of these interactions can elucid...