AIMC Topic: Molecular Dynamics Simulation

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SympGNNs: Symplectic Graph Neural Networks for identifying high-dimensional Hamiltonian systems and node classification.

Neural networks : the official journal of the International Neural Network Society Jul 1, 2025
Existing neural network models to learn Hamiltonian systems, such as SympNets, although accurate in low-dimensions, struggle to learn the correct dynamics for high-dimensional many-body systems. Herein, we introduce Symplectic Graph Neural Networks (...
Molecular Dynamics Simulation Graph Neural Networks Algorithms Computer Simulation Neural Networks, Computer
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When Simulations Meet Machine Learning: Redefining Molecular Docking for Protein-Glycosaminoglycan Systems.

Journal of computational chemistry Jun 30, 2025
Glycosaminoglycans (GAGs) are linear, negatively charged carbohydrates that modulate enzymatic activity in the extracellular matrix. Their high flexibility and specificity in protein-GAG interactions pose challenges for both experimental and computat...
Machine Learning Molecular Docking Simulation Glycosaminoglycans Proteins Ligands Molecular Dynamics Simulation Binding Sites
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NepoIP/MM: Toward Accurate Biomolecular Simulation with a Machine Learning/Molecular Mechanics Model Incorporating Polarization Effects.

Journal of chemical theory and computation Jun 10, 2025
Machine learning force fields offer the ability to simulate biomolecules with quantum mechanical accuracy while significantly reducing computational costs, attracting a growing amount of attention in biophysics. Meanwhile, by leveraging the efficienc...
Quantum Theory Dipeptides Static Electricity Proteins Molecular Dynamics Simulation Machine Learning Water
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Active Learning-Guided Hit Optimization for the Leucine-Rich Repeat Kinase 2 WDR Domain Based on In Silico Ligand-Binding Affinities.

Journal of chemical information and modeling Jun 9, 2025
The leucine-rich repeat kinase 2 (LRRK2) is the most mutated gene in familial Parkinson's disease, and its mutations lead to pathogenic hallmarks of the disease. The LRRK2 WDR domain is an understudied drug target for Parkinson's disease, with no kno...
Protein Binding Protein Domains Ligands Protein Kinase Inhibitors Molecular Dynamics Simulation Humans Machine Learning Thermodynamics Leucine-Rich Repeat Serine-Threonine Protein Kinase-2
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Investigating the Nature of PRM:SH3 Interactions Using Artificial Intelligence and Molecular Dynamics.

Journal of chemical information and modeling Jun 9, 2025
Understanding the binding interactions within protein-peptide complexes is crucial for elucidating key physicochemical phenomena in biological systems. Among the outcomes of these interactions, biomolecular condensates have recently emerged as vital ...
Protein Binding Mutation Hydrophobic and Hydrophilic Interactions src Homology Domains Artificial Intelligence Molecular Dynamics Simulation Peptides
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Using Machine Learning to Analyze Molecular Dynamics Simulations of Biomolecules.

The journal of physical chemistry. B Jun 5, 2025
Machine learning (ML) techniques have become powerful tools in both industrial and academic settings. Their ability to facilitate analysis of complex data and generation of predictive insights is transforming how scientific problems are approached ac...
Molecular Dynamics Simulation SARS-CoV-2 Angiotensin-Converting Enzyme 2 Protein Binding Spike Glycoprotein, Coronavirus Humans Machine Learning
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Rational Design of an Epoxide Hydrolase From Spatholobus Suberectus: Enhancing Catalytic Activity and Thermostability for Efficient (R)-Styrene Oxide Production.

Biotechnology journal Jun 1, 2025
(R)-Styrene oxide is a high-value chiral intermediate in pharmaceutical and chemical industries, yet its enantioselective synthesis remains challenging. Here, we engineered an epoxide hydrolase from Spatholobus suberectus (SsEH) to address its limita...
Epoxy Compounds Epoxide Hydrolases Enzyme Stability Protein Engineering Molecular Dynamics Simulation
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A hybrid protocol for peptide development: integrating deep generative models and physics simulations for biomolecular design targeting IL23R/IL23.

International journal of biological macromolecules Jun 1, 2025
Recent advances in machine learning have revolutionized molecular design; however, a gap remains in integrating generative models with physics-based simulations to develop functional modulators, such as stable peptides, for challenging targets like t...
Humans Peptides Receptors, Interleukin Interleukin-23 Protein Binding Molecular Dynamics Simulation Drug Design Deep Learning
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Multidimensional computational strategies enhance the thermostability of alpha-galactosidase.

International journal of biological macromolecules Jun 1, 2025
Alpha-Galactosidase has significant industrial application value in food processing, animal nutrition and medical applications. Microbial-derived α-galactosidases predominate industrial implementation due to high productivity, yet their inherent ther...
Molecular Dynamics Simulation Enzyme Stability Mutation Kinetics alpha-Galactosidase Protein Engineering Thermodynamics Temperature Aspergillus
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Design and molecular mechanism investigation of ALK inhibitors based on virtual screening and structural descriptor modeling.

Journal of receptor and signal transduction research Jun 1, 2025
To address the challenges of target specificity and drug resistance in Anaplastic lymphoma kinase (ALK) inhibition, this study conducted a virtual screening of the BindingDB database, yielding 711 potential ALK inhibitors. Four QSAR models were estab...
Molecular Dynamics Simulation Drug Design Humans Protein Binding Molecular Docking Simulation Quantitative Structure-Activity Relationship Anaplastic Lymphoma Kinase Protein Kinase Inhibitors
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