AIMC Topic: Binding Sites

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Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces.

Journal of chemical information and modeling Jul 2, 2025
Increasing structural and biophysical evidence suggests that many drug molecules bind to the protein-membrane interface region in membrane protein structures. An important starting point for drug discovery is the determination of a ligand's binding s...
Protein Binding Ligands Binding Sites Small Molecule Libraries Membrane Proteins Models, Molecular
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Uncertainty Quantification and Temperature Scaling Calibration for Protein-RNA Binding Site Prediction.

Journal of chemical information and modeling Jun 2, 2025
The black-box nature of deep learning has increasingly drawn attention to the reliability and uncertainty of predictive models. Currently, several uncertainty quantification (UQ) methods have been proposed and successfully applied in the fields of mo...
Binding Sites Uncertainty RNA Calibration Neural Networks, Computer Protein Binding RNA-Binding Proteins Temperature
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Molecular insights into the unique activation and allosteric modulation mechanisms of the human mas-related G-protein-coupled receptor X1.

International journal of biological macromolecules May 30, 2025
MRGPRX1 plays dual roles in mediating nociception and pruritus, making it a promising target for alleviating itch and inhibiting pain. However, the mechanisms underlying MRGPRX1 activation and allosteric modulation remain poorly understood, posing si...
Protein Binding Receptors, Neuropeptide Receptors, G-Protein-Coupled Humans Binding Sites Allosteric Regulation Molecular Dynamics Simulation Protein Conformation
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CrypToth: Cryptic Pocket Detection through Mixed-Solvent Molecular Dynamics Simulations-Based Topological Data Analysis.

Journal of chemical information and modeling May 22, 2025
Some functional proteins undergo conformational changes to expose hidden binding sites when a binding molecule approaches their surface. Such binding sites are called cryptic sites and are important targets for drug discovery. However, it is still di...
Molecular Dynamics Simulation Ligands Protein Conformation Binding Sites Solvents Proteins
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Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli.

Nature communications May 7, 2025
The DNA binding of most Escherichia coli Transcription Factors (TFs) has not been comprehensively mapped, and few have models that can quantitatively predict binding affinity. We report the global mapping of in vivo DNA binding for 139 E. coli TFs us...
Transcription Factors Escherichia coli Escherichia coli Proteins Protein Binding DNA, Bacterial Binding Sites Chromatin Immunoprecipitation Sequencing Neural Networks, Computer
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A KAN-based hybrid deep neural networks for accurate identification of transcription factor binding sites.

PloS one May 7, 2025
BACKGROUND: Predicting protein-DNA binding sites in vivo is a challenging but urgent task in many fields such as drug design and development. Most promoters contain many transcription factor (TF) binding sites, yet only a few have been identified thr...
Computational Biology Binding Sites Algorithms Transcription Factors Promoter Regions, Genetic Deep Learning Humans Protein Binding Neural Networks, Computer
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Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis.

Genome research May 2, 2025
Understanding how genetic variation impacts transcription factor (TF) binding remains a major challenge, limiting our ability to model disease-associated variants. Here, we used a highly controlled system of F crosses with extensive genetic diversity...
Drosophila melanogaster Binding Sites Drosophila Genetic Variation Embryonic Development Drosophila Proteins Transcription Factors Alleles Animals Deep Learning Protein Binding
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Dual-Site Targeting by Peptide Inhibitors of the N-Terminal Domain of Hsp90: Mechanism and Design.

Journal of chemical information and modeling May 1, 2025
Heat shock protein 90 (Hsp90) is a pivotal molecular chaperone crucial in the maturation of client proteins, positioning it as a significant target for cancer therapy. However, the design of effective Hsp90 inhibitors presents substantial challenges ...
HSP90 Heat-Shock Proteins Protein Binding Protein Domains Adenosine Triphosphate Binding Sites Molecular Dynamics Simulation Peptides Molecular Docking Simulation Drug Design Humans Machine Learning
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Enhancing Transthyretin Binding Affinity Prediction with a Consensus Model: Insights from the Tox24 Challenge.

Chemical research in toxicology Apr 26, 2025
Transthyretin (TTR) plays a vital role in thyroid hormone transport and homeostasis in both the blood and target tissues. Interactions between exogenous compounds and TTR can disrupt the function of the endocrine system, potentially causing toxicity....
Humans Deep Learning Prealbumin Binding Sites Protein Binding Ligands
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Artificial intelligence for RNA-ligand interaction prediction: advances and prospects.

Drug discovery today Apr 24, 2025
Accurate prediction of RNA-ligand interactions is vital for understanding biological processes and advancing RNA-targeted drug discovery. Given their complexity, artificial intelligence (AI) is revolutionizing the study of RNA-ligand interactions, of...
Humans Binding Sites Models, Molecular Artificial Intelligence RNA Drug Discovery Ligands
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