AIMC Topic: Thermodynamics

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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...
Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 Protein Domains Molecular Dynamics Simulation Protein Kinase Inhibitors Thermodynamics Ligands Machine Learning Protein Binding Humans
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ActiMut-XGB: Predicting thermodynamic stability of point mutations for CALB with protein language model.

International journal of biological macromolecules Jun 1, 2025
Predicting the functional impact of single-point mutations on protein residual activity, especially after high-temperature incubation, is critical in protein engineering. We present an innovative machine learning model based on eXtreme Gradient Boost...
Machine Learning Models, Molecular Fungal Proteins Protein Engineering Enzyme Stability Thermodynamics Point Mutation Lipase
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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...
Thermodynamics alpha-Galactosidase Mutation Kinetics Temperature Enzyme Stability Molecular Dynamics Simulation Aspergillus Protein Engineering
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Characterization of conformational flexibility in protein structures by applying artificial intelligence to molecular modeling.

Journal of structural biology Jun 1, 2025
Recent AI applications have revolutionized the modeling of structurally unresolved protein regions, thereby complementing traditional computational methods. These state-of-the-art techniques can generate numerous candidate structures, significantly e...
Models, Molecular Protein Folding Molecular Dynamics Simulation Artificial Intelligence Ubiquitin Protein Conformation Proteins Thermodynamics
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for Investigating Conformational Transitions and Environmental Interactions of Proteins.

Journal of chemical theory and computation May 27, 2025
Proteins are inherently dynamic molecules, and their conformational transitions among various states are essential for numerous biological processes, which are often modulated by their interactions with surrounding environments. Although molecular dy...
Molecular Dynamics Simulation Protein Conformation Proteins Thermodynamics
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Atomic Energy Accuracy of Neural Network Potentials: Harnessing Pretraining and Transfer Learning.

Journal of chemical information and modeling May 26, 2025
Machine learning-based interatomic potentials (MLIPs) have transformed the prediction of potential energy surfaces (PESs), achieving accuracy comparable to calculations. However, atomic energy predictions, often assumed to lack physical meaning, rem...
Neural Networks, Computer Machine Learning Density Functional Theory Thermodynamics
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High-Throughput Ligand Dissociation Kinetics Predictions Using Site Identification by Ligand Competitive Saturation.

Journal of chemical theory and computation May 13, 2025
The dissociation or off rate, , of a drug molecule has been shown to be more relevant to efficacy than affinity for selected systems, motivating the development of predictive computational methodologies. These are largely based on enhanced-sampling m...
Proteins Kinetics Molecular Dynamics Simulation Machine Learning Ligands Thermodynamics
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Modeling Enzyme Reaction and Mutation by Direct Machine Learning/Molecular Mechanics Simulations.

Journal of chemical theory and computation May 13, 2025
Accurately modeling enzyme reactions through direct machine learning/molecular mechanics simulations remains challenging in describing the electrostatic coupling between the QM and MM subsystems. In this work, we proposed a reweighting ME (mechanic e...
Thermodynamics Acylation Cyclooxygenase 1 Static Electricity Cyclooxygenase 2 Humans Molecular Dynamics Simulation Aspirin Machine Learning Mutation
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Including Physics-Informed Atomization Constraints in Neural Networks for Reactive Chemistry.

Journal of chemical information and modeling May 12, 2025
Machine learning interatomic potentials (MLIPs) have emerged as powerful tools for investigating atomistic systems with high accuracy and a relatively low computational cost. However, a common and unaddressed challenge with many current neural networ...
Neural Networks, Computer Thermodynamics 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 May 1, 2025
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...
Structure-Activity Relationship Machine Learning Molecular Dynamics Simulation Protein Kinase Inhibitors T-Lymphocytes Drug Discovery Humans Signal Transduction Thermodynamics Protein Binding Protein Serine-Threonine Kinases Molecular Docking Simulation
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