AIMC Topic: Protein Binding

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The EMC acts as a chaperone for membrane proteins.

Nature communications Aug 2, 2025
Structure formation of membrane proteins is error-prone and thus requires chaperones that oversee this essential process in cell biology. The ER membrane protein complex (EMC) is well-defined as a transmembrane domain (TMD) insertase. In this study, ...
Lipid Bilayers Saccharomyces cerevisiae Proteins Molecular Chaperones Endoplasmic Reticulum Membrane Proteins Protein Domains Saccharomyces cerevisiae Humans Machine Learning Protein Binding
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Sequence-based virtual screening using transformers.

Nature communications Jul 28, 2025
Protein-ligand interactions play central roles in myriad biological processes and are of key importance in drug design. Deep learning approaches are becoming cost-effective alternatives to high-throughput experimental methods for ligand identificatio...
Amino Acid Sequence Ligands Protein Conformation ErbB Receptors Protein Kinase Inhibitors Proto-Oncogene Proteins c-abl Deep Learning Protein Binding Drug Evaluation, Preclinical Humans Drug Design
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Augmenting MACCS Keys with Persistent Homology Fingerprints for Protein-Ligand Binding Classification.

Journal of chemical information and modeling Jul 25, 2025
Machine learning has become an essential tool in computational drug design, enabling models to uncover patterns in molecular data and predict protein-ligand interactions. This study introduces a novel approach by integrating persistence images with M...
Ligands Cheminformatics Drug Design Protein Binding Proteins Neural Networks, Computer Machine Learning
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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...
Signal Transduction Phenols Models, Molecular Xenopus laevis Retinoid X Receptors Computer Simulation Humans Animals Machine Learning Protein Binding Receptors, Thyroid Hormone
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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 Ligands Protein Conformation Protein Folding Protein Binding Proteins Models, Molecular
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An iterative strategy to design 4-1BB agonist nanobodies de novo with generative AI models.

Scientific reports Jul 14, 2025
The 4-1BB receptor, a key member of the tumor necrosis factor receptor (TNFR) family, represents a highly promising target for cancer immunotherapy. In this study, we developed a novel in silico pipeline to design VHH domain antibodies targeting 4-1B...
Humans Protein Binding Single-Domain Antibodies Complementarity Determining Regions Tumor Necrosis Factor Receptor Superfamily, Member 9
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CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches.

Journal of computer-aided molecular design Jul 13, 2025
Identifying orthosteric binding sites and predicting small molecule affinities remains a key challenge in virtual screening. While blind docking explores the entire protein surface, its precision is hindered by the vast search space. Cavity detection...
Protein Conformation Binding Sites Protein Binding Proteins Ligands Algorithms Machine Learning Molecular Docking Simulation Software
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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...
Iron Hemoglobins Cryoelectron Microscopy Protein Binding Heme Escherichia coli Proteins Escherichia coli Crystallography, X-Ray Models, Molecular Bacterial Outer Membrane Proteins
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Machine learning-based QSAR and structure-based virtual screening guided discovery of novel mIDH1 inhibitors from natural products.

Journal of computer-aided molecular design Jul 8, 2025
Mutations in isocitrate dehydrogenase 1 (IDH1) have been widely observed in various tumors, such as gliomas and acute myeloid leukemia, and therefore has become one of the current research focal points. Therefore, it is crucial to find inhibitors tha...
Biological Products Molecular Docking Simulation Quantitative Structure-Activity Relationship Humans Ligands Drug Discovery Isocitrate Dehydrogenase Machine Learning Enzyme Inhibitors Protein Binding Binding Sites
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Combining the NanaPPI Toolbox and AI-Driven Virtual Inhibitor Screening for the p53-MDM2 Interaction.

Analytical chemistry Jul 7, 2025
High-throughput screening for inhibitors of protein-protein interactions (PPIs) provides vital information for therapeutic intervention in diseases driven by aberrant PPIs. Traditionally, the discovery of PPI inhibitors involves sequential steps: in ...
Antineoplastic Agents Cell Line, Tumor Protein Binding Humans Artificial Intelligence Animals High-Throughput Screening Assays Tumor Suppressor Protein p53 Proto-Oncogene Proteins c-mdm2 Mice Cell Proliferation Zebrafish
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