AIMC Topic: Models, Molecular

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Evaluation of antiarrhythmia drug through QSPR modeling and multi criteria decision analysis.

Scientific reports Aug 9, 2025
This study explores how topological indices (TIs), which are mathematical descriptors of a drug's molecular structure, can support to predict vital properties and biological activities. This understanding is a key for more effective drug design. We f...
Humans Quantitative Structure-Activity Relationship Anti-Arrhythmia Agents Arrhythmias, Cardiac Decision Support Techniques Models, Molecular
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PairReg: A method for enhancing the learning of molecular structure representation in equivariant graph neural networks.

PloS one Jul 31, 2025
The 3D structure of molecules contains a wealth of important information, but traditional 3DCNN-based methods fail to adequately address the transformations of rigid motions (rotation, translation, and mapping). Equivariant graph neural networks (EGN...
Neural Networks, Computer Molecular Structure Graph Neural Networks Algorithms Models, Molecular
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Benchmarking 3D Structure-Based Molecule Generators.

Journal of chemical information and modeling Jul 25, 2025
To understand the benefits and drawbacks of 3D combinatorial and deep learning generators, a novel benchmark was created focusing on the recreation of important protein-ligand interactions and 3D ligand conformations. Using the BindingMOAD data set w...
Ligands Molecular Conformation Deep Learning Models, Molecular Benchmarking Proteins
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Assisting and accelerating NMR assignment with restrained structure prediction.

Communications biology Jul 18, 2025
Accurate dynamic protein structures are essential for drug design. NMR experiments can detect protein structures and potential dynamics, but the spectrum assignment and structure determination requires expertise and is time-consuming, while deep-lear...
Models, Molecular Protein Conformation Magnetic Resonance Spectroscopy Protein Folding Nuclear Magnetic Resonance, Biomolecular Proteins
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An in silico to in vivo approach identifies retinoid-X receptor activating tert-butylphenols used in food contact materials.

Scientific reports Jul 18, 2025
The potential for food contact chemicals to disrupt genetic programs in development and metabolism raises concerns. Nuclear receptors (NRs) control many of these programs, and the retinoid-X receptor (RXR) is a DNA-binding partner for one-third of th...
Receptors, Thyroid Hormone Xenopus laevis Retinoid X Receptors Protein Binding Signal Transduction Phenols Models, Molecular Computer Simulation Animals Humans Machine Learning
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Graph Convolutional Neural Network-Enabled Frontier Molecular Orbital Prediction: A Case Study with Neurotransmitters and Antidepressants.

Journal of chemical information and modeling Jul 17, 2025
With the advancement of artificial intelligence-embedded methodologies, their application to predict fundamental molecular properties has become increasingly prevalent. In this study, a graph convolutional neural network fingerprint-enabled artificia...
Humans Neural Networks, Computer Convolutional Neural Networks Neurotransmitter Agents Antidepressive Agents Models, Molecular Thermodynamics
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AI to rewire life's interactome: Structural foundation models help to elucidate and reprogram molecular biology.

Science (New York, N.Y.) Jul 17, 2025
Structural foundation models help to elucidate and reprogram molecular biology.
Models, Molecular Molecular Biology Humans Artificial Intelligence
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AF3Score: A Score-Only Adaptation of AlphaFold3 for Biomolecular Structure Evaluation.

Journal of chemical information and modeling Jul 16, 2025
Scoring biomolecular complexes remains central to structural modeling efforts. Recent studies suggest that AlphaFold (AF) - a revolutionary deep learning model for biomolecular structure prediction - has implicitly learned an approximate biophysical ...
Deep Learning Protein Binding Ligands Protein Conformation Protein Folding Proteins Models, Molecular
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Epi4Ab: a data-driven prediction model of conformational epitopes for specific antibody VH/VL families and CDRs sequences.

mAbs Jul 10, 2025
Antibodies recognize antigens via complementary and structurally dependent mechanisms. Therefore, inclusion of antibody inputs is crucial for accurate epitope prediction. Given the limited availability of antibody-antigen complex structures, any epit...
Humans Models, Molecular Immunoglobulin Light Chains Immunoglobulin Variable Region Immunoglobulin Heavy Chains Epitopes Complementarity Determining Regions
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Inhibiting heme piracy by pathogenic Escherichia coli using de novo-designed proteins.

Nature communications Jul 9, 2025
Iron is an essential nutrient for most bacteria and is often growth-limiting during infection, due to the host sequestering free iron as part of the innate immune response. To obtain the iron required for growth, many bacterial pathogens encode trans...
Bacterial Outer Membrane Proteins Hemoglobins Cryoelectron Microscopy Models, Molecular Protein Binding Escherichia coli Proteins Iron Heme Escherichia coli Crystallography, X-Ray
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