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Molecular Docking Simulation

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Bioactivity predictions and virtual screening using machine learning predictive model.

Journal of biomolecular structure & dynamics Jan 12, 2024
Recently, there has been significant attention on machine learning algorithms for predictive modeling. Prediction models for enzyme inhibitors are limited, and it is essential to account for chemical biases while developing them. The lack of repeatab...
Algorithms Molecular Dynamics Simulation Molecular Docking Simulation Drug Evaluation, Preclinical Drug Discovery Dipeptidyl Peptidase 4 Humans Dipeptidyl-Peptidase IV Inhibitors Machine Learning
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Discovery of hematopoietic progenitor kinase 1 inhibitors using machine learning-based screening and free energy perturbation.

Journal of biomolecular structure & dynamics Jan 10, 2024
Hematopoietic progenitor kinase 1 (HPK1) is a key negative regulator of T-cell receptor (TCR) signaling and a promising target for cancer immunotherapy. The development of novel HPK1 inhibitors is challenging yet promising. In this study, we used a c...
Molecular Docking Simulation Drug Discovery Protein Binding Signal Transduction Humans Machine Learning T-Lymphocytes Protein Kinase Inhibitors Thermodynamics Protein Serine-Threonine Kinases Structure-Activity Relationship Molecular Dynamics Simulation
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Explainable artificial intelligence-assisted virtual screening and bioinformatics approaches for effective bioactivity prediction of phenolic cyclooxygenase-2 (COX-2) inhibitors using PubChem molecular fingerprints.

Molecular diversity Jan 10, 2024
Cyclooxygenase-2 (COX-2) inhibitors are nonsteroidal anti-inflammatory drugs that treat inflammation, pain and fever. This study determined the interaction mechanisms of COX-2 inhibitors and the molecular properties needed to design new drug candidat...
Ligands Hydrophobic and Hydrophilic Interactions Cyclooxygenase 2 Inhibitors Cyclooxygenase 2 Computational Biology Phenols Molecular Dynamics Simulation Machine Learning Molecular Docking Simulation Artificial Intelligence
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Integrative analysis of potential diagnostic markers and therapeutic targets for glomerulus-associated diabetic nephropathy based on cellular senescence.

Frontiers in immunology Jan 8, 2024
INTRODUCTION: Diabetic nephropathy (DN), distinguished by detrimental changes in the renal glomeruli, is regarded as the leading cause of death from end-stage renal disease among diabetics. Cellular senescence plays a paramount role, profoundly affec...
Aged Animals Molecular Docking Simulation Mice Kidney Glomerulus Humans Diabetic Nephropathies Forkhead Transcription Factors Renal Insufficiency, Chronic Cellular Senescence Diabetes Mellitus
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T6496 targeting EGFR mediated by T790M or C797S mutant: machine learning, virtual screening and bioactivity evaluation study.

Journal of biomolecular structure & dynamics Jan 4, 2024
Acquired resistance to EGFR is a major impediment in lung cancer treatment, highlighting the urgent need to discover novel compounds to overcome EGFR drug resistance. In this study, we utilized in silico methods and bioactivity evaluation for drug di...
ErbB Receptors Protein Kinase Inhibitors Molecular Docking Simulation Drug Screening Assays, Antitumor Drug Discovery Mutation Antineoplastic Agents Drug Resistance, Neoplasm Cell Proliferation Humans Apoptosis Cell Line, Tumor Machine Learning Protein Binding
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Using deep learning and molecular dynamics simulations to unravel the regulation mechanism of peptides as noncompetitive inhibitor of xanthine oxidase.

Scientific reports Jan 2, 2024
Xanthine oxidase (XO) is a crucial enzyme in the development of hyperuricemia and gout. This study focuses on LWM and ALPM, two food-derived inhibitors of XO. We used molecular docking to obtain three systems and then conducted 200 ns molecular dynam...
Humans Peptides Hyperuricemia Molecular Dynamics Simulation Enzyme Inhibitors Xanthine Oxidase Molecular Docking Simulation Deep Learning Structure-Activity Relationship
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Specneuzhenide improves bleomycin-induced pulmonary fibrosis in mice via AMPK-dependent reduction of PD-L1.

Phytomedicine : international journal of phytotherapy and phytopharmacology Dec 30, 2023
BACKGROUND: Pulmonary fibrosis (PF) is an escalating global health issue, characterized by rising rates of morbidity and mortality annually. Consequently, further investigation of potential damage mechanisms and potential preventive strategies for PF...
Disease Models, Animal Epithelial-Mesenchymal Transition Bleomycin Pulmonary Fibrosis Transforming Growth Factor beta1 Fibroblasts Molecular Docking Simulation Animals AMP-Activated Protein Kinases Mice, Inbred C57BL Male Cell Line B7-H1 Antigen Lung Mice
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Harnessing deep learning for enhanced ligand docking.

Trends in pharmacological sciences Dec 30, 2023
Ligand docking (LD), a technology for predicting protein-ligand (PL)-binding conformations and strengths, plays key roles in virtual screening (VS). However, the accuracy and speed of current LD methodologies remain suboptimal. Here, we discuss how d...
Proteins Ligands Humans Protein Conformation Molecular Docking Simulation Deep Learning Protein Binding
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Investigating the bispecific lead compounds against methicillin-resistant SarA and CrtM using machine learning and molecular dynamics approach.

Journal of biomolecular structure & dynamics Dec 26, 2023
Methicillin-resistant Staphylococcus aureus (MRSA) is a notorious pathogen that has emerged as a serious global health concern over the past few decades. Staphylococcal accessory regulator A (SarA) and 4,4'-diapophytoene synthase (CrtM) play a crucia...
Machine Learning Anti-Bacterial Agents Molecular Docking Simulation Methicillin-Resistant Staphylococcus aureus Bacterial Proteins Biofilms Protein Binding Molecular Dynamics Simulation Quantitative Structure-Activity Relationship Hydrogen Bonding
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Deep learning-based design and screening of benzimidazole-pyrazine derivatives as adenosine A receptor antagonists.

Journal of biomolecular structure & dynamics Dec 22, 2023
The Adenosine A receptor (AAR) is considered a novel potential target for the immunotherapy of cancer, and AAR antagonists have an inhibitory effect on tumor growth, proliferation, and metastasis. In our previous studies, we identified a class of ben...
Receptor, Adenosine A2B Protein Binding Pyrazines Structure-Activity Relationship Benzimidazoles Adenosine A2 Receptor Antagonists Molecular Structure Molecular Dynamics Simulation Humans Drug Design Molecular Docking Simulation Deep Learning
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