AI Medical Compendium Journal:
Physical chemistry chemical physics : PCCP

Showing 1 to 10 of 37 articles

Machine learning models for predicting configuration of modified knuckle epitope peptides of BMP-2 protein using mesoscale simulation data.

Physical chemistry chemical physics : PCCP Apr 30, 2025
The high doses of bone morphogenetic proteins (BMPs) cause undesired side effects in skeletal tissue regeneration. An alternative approach is to use the bioactive knuckle epitope domain of BMP-2 (BMP2-KEP) with an open-arm structure as part of the pr...
Machine Learning Peptides Humans Amino Acid Sequence Quantitative Structure-Activity Relationship Models, Molecular Bone Morphogenetic Protein 2 Epitopes
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Insights into phosphorylation-induced influences on conformations and inhibitor binding of CDK6 through GaMD trajectory-based deep learning.

Physical chemistry chemical physics : PCCP Mar 26, 2025
The phosphorylation of residue T177 produces a significant effect on the conformational dynamics of CDK6. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) are applied to explore the molecular mechanism of the ...
Cyclin-Dependent Kinase 6 Phosphorylation Molecular Dynamics Simulation Protein Kinase Inhibitors Thermodynamics Deep Learning Humans Protein Binding Protein Conformation
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Based on T.E.S.T toxicity prediction and machine learning to forecast toxicity dynamics in the photocatalytic degradation of tetracycline.

Physical chemistry chemical physics : PCCP Nov 13, 2024
The integration of photocatalysis and biological treatment provides an effective strategy for controlling antibiotic contamination, which requires precise monitoring of toxicity changes during the photocatalytic process. In this study, nanoscale TiO ...
Machine Learning Anti-Bacterial Agents Titanium Photolysis Photochemical Processes Reactive Oxygen Species Catalysis Tetracycline
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pH-Controlled enzymatic computing for digital circuits and neural networks.

Physical chemistry chemical physics : PCCP Aug 7, 2024
Unconventional computing paradigms explore new methods for processing information beyond the capabilities of traditional electronic architectures. In this work, we present our approach to digital computation through enzymatic reactions in chemically ...
Hydrogen-Ion Concentration Enzymes Neural Networks, Computer
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Machine learning-aided engineering of a cytochrome P450 for optimal bioconversion of lignin fragments.

Physical chemistry chemical physics : PCCP Jun 26, 2024
Using machine learning, molecular dynamics simulations, and density functional theory calculations we gain insight into the selectivity patterns of substrate activation by the cytochromes P450. In nature, the reactions catalyzed by the P450s lead to ...
Density Functional Theory Molecular Dynamics Simulation Lignin Cytochrome P-450 Enzyme System Machine Learning Protein Engineering
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An active machine learning discovery platform for membrane-disrupting and pore-forming peptides.

Physical chemistry chemical physics : PCCP Jun 26, 2024
Membrane-disrupting and pore-forming peptides (PFPs) play a substantial role in bionanotechnology and can determine the life and death of cells. The control of chemical and ion transport through cell membranes is essential to maintaining concentratio...
Lipid Bilayers Pore Forming Cytotoxic Proteins Peptides Cell Membrane Machine Learning
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Application of molecular dynamics-based pharmacophore and machine learning approaches to identify novel Mcl1 inhibitors through drug repurposing and mechanics research.

Physical chemistry chemical physics : PCCP Jun 6, 2024
Myeloid cell leukemia 1 (Mcl1), a critical protein that regulates apoptosis, has been considered as a promising target for antitumor drugs. The conventional pharmacophore screening approach has limitations in conformation sampling and data mining. He...
Fluvastatin Myeloid Cell Leukemia Sequence 1 Protein Pharmacophore Molecular Dynamics Simulation Quantum Theory Cell Line, Tumor Drug Repositioning Machine Learning Antineoplastic Agents Humans
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Interface design of SARS-CoV-2 symmetrical nsp7 dimer and machine learning-guided nsp7 sequence prediction reveals physicochemical properties and hotspots for nsp7 stability, adaptation, and therapeutic design.

Physical chemistry chemical physics : PCCP May 8, 2024
The COVID-19 pandemic, driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), necessitates a profound understanding of the virus and its lifecycle. As an RNA virus with high mutation rates, SARS-CoV-2 exhibits genetic variability lea...
Coronavirus RNA-Dependent RNA Polymerase Humans Viral Nonstructural Proteins SARS-CoV-2 Protein Multimerization Mutation Amino Acid Sequence Machine Learning COVID-19
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A novel activation function based on DNA enzyme-free hybridization reaction and its implementation on nonlinear molecular learning systems.

Physical chemistry chemical physics : PCCP Apr 17, 2024
With the advent of the post-Moore's Law era, the development of traditional silicon-based computers has reached its limit, and there is an urgent need to develop new computing technologies to meet the needs of science, technology, and daily life. Due...
DNA Computers, Molecular Artificial Intelligence Humans Computers Neural Networks, Computer
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On machine learning analysis of atomic force microscopy images for image classification, sample surface recognition.

Physical chemistry chemical physics : PCCP Apr 17, 2024
Atomic force microscopy (AFM or SPM) imaging is one of the best matches with machine learning (ML) analysis among microscopy techniques. The digital format of AFM images allows for direct utilization in ML algorithms without the need for additional p...
Microscopy, Atomic Force Algorithms Prospective Studies Neural Networks, Computer Machine Learning
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