AIMC Topic: Molecular Dynamics Simulation

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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 Docking Simulation Molecular Dynamics 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 Immune Checkpoint Inhibitors B7-H1 Antigen Signal Transduction Machine Learning Molecular Docking Simulation Drug Design Programmed Cell Death 1 Receptor Molecular Dynamics Simulation Small Molecule Libraries Ligands
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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,...
SELEX Aptamer Technique Molecular Dynamics Simulation High-Throughput Screening Assays Machine Learning Aptamers, Nucleotide Humans Molecular Docking Simulation Biosensing Techniques Drug Design Computational Biology
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Exploring Protein Conformational Changes Using a Large-Scale Biophysical Sampling Augmented Deep Learning Strategy.

Advanced science (Weinheim, Baden-Wurttemberg, Germany) Oct 10, 2024
Inspired by the success of deep learning in predicting static protein structures, researchers are now actively exploring other deep learning algorithms aimed at predicting the conformational changes of proteins. Currently, a major challenge in the de...
Molecular Dynamics Simulation Protein Conformation Deep Learning Proteins Humans Algorithms
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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...
Molecular Dynamics Simulation Quantitative Structure-Activity Relationship Cathepsin K Molecular Docking Simulation Drug Design Machine Learning
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A computational and machine learning approach to identify GPR40-targeting agonists for neurodegenerative disease treatment.

PloS one Oct 8, 2024
The G protein-coupled receptor 40 (GPR40) is known to exert a significant influence on neurogenesis and neurodevelopment within the central nervous system of both humans and rodents. Research findings indicate that the activation of GPR40 by an agoni...
Neurodegenerative Diseases Molecular Docking Simulation Humans Molecular Dynamics Simulation Protein Binding Machine Learning Ligands Receptors, G-Protein-Coupled Thermodynamics
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Deep learning for discriminating non-trivial conformational changes in molecular dynamics simulations of SARS-CoV-2 spike-ACE2.

Scientific reports Sep 30, 2024
Molecular dynamics (MD) simulations produce a substantial volume of high-dimensional data, and traditional methods for analyzing these data pose significant computational demands. Advances in MD simulation analysis combined with deep learning-based a...
Deep Learning Protein Binding Spike Glycoprotein, Coronavirus Mutation Protein Domains Humans COVID-19 SARS-CoV-2 Angiotensin-Converting Enzyme 2 Molecular Dynamics Simulation Binding Sites Protein Conformation
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Recursive dynamics of GspE through machine learning enabled identification of inhibitors.

Computational biology and chemistry Sep 28, 2024
Type II secretion System has been increasingly recognized as a key driver of virulence in many pathogenic bacteria including Achromobacter xylosoxidans. ATPase GspE is the powerhouse of the T2SS. It powers the entire secretion process by binding with...
Enzyme Inhibitors Adenosine Triphosphatases Microbial Sensitivity Tests Molecular Structure Molecular Dynamics Simulation Machine Learning Anti-Bacterial Agents Molecular Docking Simulation
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Development of a machine learning-based target-specific scoring function for structure-based binding affinity prediction for human dihydroorotate dehydrogenase inhibitors.

Journal of computational chemistry Sep 26, 2024
Human dihydroorotate dehydrogenase (hDHODH) is a flavin mononucleotide-dependent enzyme that can limit de novo pyrimidine synthesis, making it a therapeutic target for diseases such as autoimmune disorders and cancer. In this study, using the docking...
Dihydroorotate Dehydrogenase Oxidoreductases Acting on CH-CH Group Donors Enzyme Inhibitors Binding Sites Machine Learning Molecular Docking Simulation Protein Binding Molecular Structure Molecular Dynamics Simulation Ligands Humans
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Nutmeg and SPICE: Models and Data for Biomolecular Machine Learning.

Journal of chemical theory and computation Sep 25, 2024
We describe version 2 of the SPICE data set, a collection of quantum chemistry calculations for training machine learning potentials. It expands on the original data set by adding much more sampling of chemical space and more data on noncovalent inte...
Molecular Dynamics Simulation Quantum Theory Thermodynamics Machine Learning
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