AIMC Topic: Quantum Theory

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A semiempirical and machine learning approach for fragment-based structural analysis of non-hydroxamate HDAC3 inhibitors.

Biophysical chemistry Feb 15, 2025
Interest in HDAC3 inhibitors (HDAC3i) for pharmacological applications outside of cancer is growing. However, concerns regarding the possible mutagenicity of the commonly used hydroxamates (zinc-binding groups, ZBGs) are also increasing. Considering ...
Humans Machine Learning Quantitative Structure-Activity Relationship Molecular Dynamics Simulation Thermodynamics Quantum Theory Histone Deacetylase Inhibitors Molecular Docking Simulation Histone Deacetylases Molecular Structure
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Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design.

Journal of chemical information and modeling Feb 10, 2025
Computational enzyme design is a promising technique for producing novel enzymes for industrial and clinical needs. A key challenge that this technique faces is to consistently achieve the desired activity. Fundamental studies of natural enzymes reve...
Quantum Theory Biocatalysis Machine Learning Models, Molecular Static Electricity Protein Engineering Catalytic Domain Serine Proteases
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Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation.

Journal of chemical information and modeling Jan 28, 2025
In the field of computational chemistry, predicting bond dissociation energies (BDEs) presents well-known challenges, particularly due to the multireference character of reactive systems. Many chemical reactions involve configurations where single-re...
Thermodynamics Methane Quantum Theory Machine Learning
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Deep Learning of CYP450 Binding of Small Molecules by Quantum Information.

Journal of chemical information and modeling Jan 27, 2025
Drug-drug interaction can lead to diminished therapeutic effects or increased toxicity, posing significant risks, especially in polypharmacy, and cytochrome P450 plays an indispensable role in this interaction. Cytochrome P450, responsible for the me...
Cytochrome P-450 Enzyme System Humans Cytochrome P-450 CYP1A2 Small Molecule Libraries Deep Learning Drug Interactions Protein Binding Quantum Theory
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Enhancing Activation Energy Predictions under Data Constraints Using Graph Neural Networks.

Journal of chemical information and modeling Jan 25, 2025
Accurately predicting activation energies is crucial for understanding chemical reactions and modeling complex reaction systems. However, the high computational cost of quantum chemistry methods often limits the feasibility of large-scale studies, le...
Thermodynamics Graph Neural Networks Machine Learning Neural Networks, Computer Quantum Theory
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Machine Learning Quantum Mechanical/Molecular Mechanical Potentials: Evaluating Transferability in Dihydrofolate Reductase-Catalyzed Reactions.

Journal of chemical theory and computation Jan 15, 2025
Integrating machine learning potentials (MLPs) with quantum mechanical/molecular mechanical (QM/MM) free energy simulations has emerged as a powerful approach for studying enzymatic catalysis. However, its practical application has been hindered by t...
Thermodynamics Tetrahydrofolate Dehydrogenase Quantum Theory Machine Learning Biocatalysis Molecular Dynamics Simulation
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Machine Learning Recognition of Artificial DNA Sequence with Quantum Tunneling Nanogap Junction.

The journal of physical chemistry. B Jan 9, 2025
Artificially synthesized DNA holds significant promise in addressing fundamental biochemical questions and driving advancements in biotechnology, genetics, and DNA digital data storage. Rapid and precise electric identification of these artificial DN...
Quantum Theory Machine Learning DNA
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Quantum mixed-state self-attention network.

Neural networks : the official journal of the International Neural Network Society Jan 8, 2025
Attention mechanisms have revolutionized natural language processing. Combining them with quantum computing aims to further advance this technology. This paper introduces a novel Quantum Mixed-State Self-Attention Network (QMSAN) for natural language...
Algorithms Natural Language Processing Quantum Theory Attention Humans Neural Networks, Computer
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High-Accuracy Identification and Structure-Activity Analysis of Antioxidant Peptides via Deep Learning and Quantum Chemistry.

Journal of chemical information and modeling Jan 7, 2025
Antioxidant peptides (AOPs) hold great promise for mitigating oxidative-stress-related diseases, but their discovery is hindered by inefficient and time-consuming traditional methods. To address this, we developed an innovative framework combining ma...
Antioxidants Structure-Activity Relationship Quantum Theory Peptides Deep Learning
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Evaluation of Machine Learning/Molecular Mechanics End-State Corrections with Mechanical Embedding to Calculate Relative Protein-Ligand Binding Free Energies.

Journal of chemical theory and computation Jan 3, 2025
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are several ti...
Molecular Dynamics Simulation Quantum Theory Protein Binding Proteins Ligands Thermodynamics Machine Learning
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