AIMC Topic: Molecular Docking Simulation

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Tackling APOE's structural challenges via in silico modeling in the era of neural networks: Can AlphaFold II help circumvent the problem of lacking full-length protein structure?

Archives of biochemistry and biophysics Oct 22, 2024
The APOE gene, encoding apolipoprotein E, is a predictor of longevity and age-related diseases. Despite numerous genetic studies, the data on molecular mechanisms by which apolipoprotein E affects the human phenotype remain incomplete due to the stru...
Humans Protein Conformation Apolipoproteins E Molecular Docking Simulation Neural Networks, Computer Molecular Dynamics Simulation
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Computational screening of umami tastants using deep learning.

Molecular diversity Oct 18, 2024
Umami, a fundamental human taste modality, refers to the savory flavors in meats and broths, often associated with monosodium glutamate and protein richness. With limited knowledge of umami molecules, the food industry seeks efficient approaches for ...
Flavoring Agents Receptors, G-Protein-Coupled Taste Humans Molecular Docking Simulation Neural Networks, Computer Deep Learning
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Machine learning-based identification and validation of immune-related biomarkers for early diagnosis and targeted therapy in diabetic retinopathy.

Gene Oct 18, 2024
The early diagnosis of diabetic retinopathy (DR) is challenging, highlighting the urgent need to identify new biomarkers. Immune responses play a crucial role in DR, yet there are currently no reports of machine learning (ML) algorithms being utilize...
Humans Algorithms Biomarkers Molecular Docking Simulation Diabetic Retinopathy Machine Learning Support Vector Machine Molecular Targeted Therapy Bayes Theorem Early Diagnosis Gene Expression Profiling Gene Regulatory Networks
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Machine learning models to identify lead compound and substitution optimization to have derived energetics and conformational stability through docking and MD simulations for sphingosine kinase 1.

Molecular diversity Oct 17, 2024
Sphingosine kinases (SphKs) are a group of important enzymes that circulate at low micromolar concentrations in mammals and have received considerable attention due to the roles they play in a broad array of biological processes including apoptosis, ...
Humans Machine Learning Hydrogen Bonding Thermodynamics Phosphotransferases (Alcohol Group Acceptor) Molecular Dynamics Simulation Molecular Docking Simulation Enzyme Inhibitors
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Towards novel small-molecule inhibitors blocking PD-1/PD-L1 pathway: From explainable machine learning models to molecular dynamics simulation.

International journal of biological macromolecules Oct 15, 2024
Molecular design of small-molecule inhibitors targeting programmed cell death-1 (PD-1)/programmed cell death ligand-1 (PD-L1) pathway has been recognized as an active research area by the clinical success of cancer immunotherapy. In recent years, usi...
Humans Machine Learning Drug Design Immune Checkpoint Inhibitors Molecular Docking Simulation Small Molecule Libraries Molecular Dynamics Simulation B7-H1 Antigen Signal Transduction Ligands Programmed Cell Death 1 Receptor
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Integration of 3D-QSAR, molecular docking, and machine learning techniques for rational design of nicotinamide-based SIRT2 inhibitors.

Computational biology and chemistry Oct 10, 2024
Selective inhibitors of sirtuin-2 (SIRT2) are increasingly recognized as potential therapeutics for cancer and neurodegenerative diseases. Derivatives of 5-((3-amidobenzyl)oxy)nicotinamides have been identified as some of the most potent and selectiv...
Quantitative Structure-Activity Relationship Niacinamide Enzyme Inhibitors Sirtuin 2 Humans Machine Learning Drug Design Molecular Structure Molecular Docking Simulation
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High-throughput and computational techniques for aptamer design.

Expert opinion on drug discovery Oct 10, 2024
INTRODUCTION: Aptamers refer to short ssDNA/RNA sequences that target small molecules, proteins, or cells. Aptamers have significantly advanced diagnostic applications, including biosensors for detecting specific biomarkers, state-of-the-art imaging,...
High-Throughput Screening Assays SELEX Aptamer Technique Computational Biology Molecular Dynamics Simulation Machine Learning Molecular Docking Simulation Aptamers, Nucleotide Biosensing Techniques Humans Drug Design
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Deep convolutional neural network-based identification and biological evaluation of MAO-B inhibitors.

International journal of biological macromolecules Oct 9, 2024
Parkinson's disease (PD) is one of the most prominent motor disorder of adult-onset dementia connected to memory and other cognitive abilities. Individuals with this vicious neurodegenerative condition tend to have an elevated expression of Monoamine...
Humans Monoamine Oxidase Inhibitors Neural Networks, Computer Deep Learning Molecular Docking Simulation Monoamine Oxidase
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Identification of endocrine-disrupting chemicals targeting key OP-associated genes via bioinformatics and machine learning.

Ecotoxicology and environmental safety Oct 9, 2024
Osteoporosis (OP), a metabolic disorder predominantly impacting postmenopausal women, has seen considerable progress in diagnosis and treatment over the past few decades. However, the intricate interplay between genetic factors and endocrine disrupto...
Computational Biology Humans Environmental Pollutants Machine Learning Endocrine Disruptors Female Molecular Docking Simulation
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Deciphering Cathepsin K inhibitors: a combined QSAR, docking and MD simulation based machine learning approaches for drug design.

SAR and QSAR in environmental research Oct 9, 2024
Cathepsin K (CatK), a lysosomal cysteine protease, contributes to skeletal abnormalities, heart diseases, lung inflammation, and central nervous system and immune disorders. Currently, CatK inhibitors are associated with severe adverse effects, there...
Cathepsin K Drug Design Machine Learning Molecular Dynamics Simulation Molecular Docking Simulation Quantitative Structure-Activity Relationship
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