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Molecular Docking Simulation

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FitScore: a fast machine learning-based score for 3D virtual screening enrichment.

Journal of computer-aided molecular design Aug 16, 2024
Enhancing virtual screening enrichment has become an urgent problem in computational chemistry, driven by increasingly large databases of commercially available compounds, without a commensurate drop in in vitro screening costs. Docking these large d...
Proteins Drug Evaluation, Preclinical Ligands Molecular Docking Simulation Drug Discovery Protein Binding Binding Sites Humans Machine Learning Software
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Identification of mycobacterial Thymidylate kinase inhibitors: a comprehensive pharmacophore, machine learning, molecular docking, and molecular dynamics simulation studies.

Molecular diversity Aug 16, 2024
Thymidylate kinase (TMK) is a pivotal enzyme in Mycobacterium tuberculosis (Mtb), crucial for phosphorylating thymidine monophosphate (dTMP) to thymidine diphosphate (dTDP), thereby playing a critical role in DNA biosynthesis. Dysregulation or inhibi...
Pharmacophore Protein Binding Antitubercular Agents Molecular Dynamics Simulation Machine Learning Molecular Docking Simulation Mycobacterium tuberculosis Protein Kinase Inhibitors Enzyme Inhibitors Nucleoside-Phosphate Kinase
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Discovery of novel ULK1 inhibitors through machine learning-guided virtual screening and biological evaluation.

Future medicinal chemistry Aug 15, 2024
Build a virtual screening model for ULK1 inhibitors based on artificial intelligence. Build machine learning and deep learning classification models and combine molecular docking and biological evaluation to screen ULK1 inhibitors from 13 million co...
Molecular Dynamics Simulation Drug Evaluation, Preclinical Humans Intracellular Signaling Peptides and Proteins Molecular Docking Simulation Protein Kinase Inhibitors Machine Learning Autophagy-Related Protein-1 Homolog Drug Discovery Molecular Structure
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E-pharmacophore and deep learning based high throughput virtual screening for identification of CDPK1 inhibitors of Cryptosporidium parvum.

Computational biology and chemistry Aug 13, 2024
Cryptosporidiosis, a prevalent gastrointestinal illness worldwide, is caused by the protozoan parasite Cryptosporidium parvum. Calcium-dependent protein kinase 1 (CpCDPK1), crucial for the parasite's life cycle, serves as a promising drug target due ...
Molecular Docking Simulation Deep Learning Molecular Structure Drug Evaluation, Preclinical Protein Kinases High-Throughput Screening Assays Pharmacophore Antiprotozoal Agents Protein Kinase Inhibitors Cryptosporidium parvum
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Mechanisms of QingRe HuoXue Formula in atherosclerosis Treatment: An integrated approach using Bioinformatics, Machine Learning, and experimental validation.

International immunopharmacology Aug 12, 2024
BACKGROUND: Atherosclerosis (AS) is the main cause of coronary heart disease, cerebral infarction, and peripheral vascular disease. QingRe HuoXue Formula (QRHXF), a common prescription of traditional Chinese medicine, has a definite effect on the cli...
Animals Male Molecular Docking Simulation Gene Expression Profiling Humans Machine Learning Plaque, Atherosclerotic Collagen Type I Collagen Type I, alpha 1 Chain Mice, Inbred C57BL Drugs, Chinese Herbal Atherosclerosis Mice Computational Biology Disease Models, Animal
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Combining machine learning, molecular dynamics, and free energy analysis for (5HT)-2A receptor modulator classification.

Journal of molecular graphics & modelling Aug 5, 2024
The 5-Hydroxytryptamine (5HT)-2A receptor, a key target in psychoactive drug development, presents significant challenges in the design of selective compounds. Here, we describe the construction, evaluation and validation of two machine learning (ML)...
Molecular Dynamics Simulation Receptor, Serotonin, 5-HT2A Thermodynamics Molecular Docking Simulation Drug Discovery Protein Binding Humans Machine Learning
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Virtual-screening of xanthine oxidase inhibitory peptides: Inhibition mechanisms and prediction of activity using machine-learning.

Food chemistry Aug 3, 2024
Xanthine oxidase (XO) inhibitory peptides can prevent XO-mediated hyperuricemia. Currently, QSAR about XO inhibitory peptides with different lengths remains to be enriched. Here, XO inhibitory peptides were obtained from porcine visceral proteins thr...
Quantitative Structure-Activity Relationship Binding Sites Xanthine Oxidase Molecular Docking Simulation Swine Machine Learning Enzyme Inhibitors Animals Peptides
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Cheminformatics analysis of indoleamine and tryptophan 2,3-dioxygenase inhibitors: A descriptor and fingerprint based machine learning approach to disclose selectivity measures.

Computers in biology and medicine Aug 1, 2024
Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are attractive drug targets for cancer immunotherapy. After disappointing results of the epacadostat as a selective IDO inhibitor in phase III clinical trials, there is much inter...
Enzyme Inhibitors Indoleamine-Pyrrole 2,3,-Dioxygenase Cheminformatics Tryptophan Oxygenase Humans Machine Learning Molecular Docking Simulation
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Identification of programmed cell death-related genes and diagnostic biomarkers in endometriosis using a machine learning and Mendelian randomization approach.

Frontiers in endocrinology Aug 1, 2024
BACKGROUND: Endometriosis (EM) is a prevalent gynecological disorder frequently associated with irregular menstruation and infertility. Programmed cell death (PCD) is pivotal in the pathophysiological mechanisms underlying EM. Despite this, the preci...
Apoptosis Female Mendelian Randomization Analysis Humans Pyruvate Dehydrogenase Acetyl-Transferring Kinase Endometriosis Molecular Docking Simulation Machine Learning Gene Expression Profiling Biomarkers
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Combined structure-based virtual screening and machine learning approach for the identification of potential dual inhibitors of ACC and DGAT2.

International journal of biological macromolecules Jul 31, 2024
Acetyl-coenzyme A carboxylase (ACC) and diacylglycerol acyltransferase 2 (DGAT2) are recognized as potential therapeutic targets for nonalcoholic fatty liver disease (NAFLD). Inhibitors targeting ACC and DGAT2 have exhibited the capacity to reduce he...
Binding Sites Diacylglycerol O-Acyltransferase Acetyl-CoA Carboxylase Drug Evaluation, Preclinical Non-alcoholic Fatty Liver Disease Enzyme Inhibitors Machine Learning Molecular Docking Simulation Protein Binding Humans Molecular Dynamics Simulation
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