AIMC Topic: Protein Binding

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On the Difficulty to Rescore Hits from Ultralarge Docking Screens.

Journal of chemical information and modeling May 22, 2025
Docking-based virtual screening tools customized to mine ultralarge chemical spaces are consistently reported to yield both higher hit rates and more potent ligands than that achieved by conventional docking of smaller million-sized compound librarie...
Protein Binding Proteins Drug Evaluation, Preclinical Machine Learning Molecular Docking Simulation Quantum Theory Ligands
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Assessing the generalization capabilities of TCR binding predictors via peptide distance analysis.

PloS one May 20, 2025
Understanding the interaction between T Cell Receptors (TCRs) and peptide-bound Major Histocompatibility Complexes (pMHCs) is crucial for comprehending immune responses and developing targeted immunotherapies. While recent machine learning (ML) model...
Machine Learning Algorithms Receptors, Antigen, T-Cell Protein Binding Peptides Humans
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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...
Binding Sites Chromatin Immunoprecipitation Sequencing Transcription Factors Escherichia coli Neural Networks, Computer Protein Binding DNA, Bacterial Escherichia coli Proteins
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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 Transcription Factors Algorithms Deep Learning Binding Sites Humans Promoter Regions, Genetic 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...
Deep Learning Protein Binding Animals Drosophila melanogaster Binding Sites Drosophila Embryonic Development Genetic Variation Transcription Factors Drosophila Proteins Alleles
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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 ...
Humans Machine Learning Peptides Adenosine Triphosphate Protein Binding HSP90 Heat-Shock Proteins Molecular Docking Simulation Protein Domains Binding Sites Drug Design Molecular Dynamics Simulation
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AdptDilatedGCN: Protein-ligand binding affinity prediction based on multi-scale interaction fusion mechanism and dilated GCN.

International journal of biological macromolecules Apr 30, 2025
Predicting protein-ligand binding affinity is crucial for drug discovery. However, existing prediction methods often make insufficient use of the features of proteins and ligands, lack interactions between different information, and have difficulty i...
Ligands Computational Biology Deep Learning Proteins Protein Binding
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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....
Prealbumin Binding Sites Protein Binding Ligands Humans Deep Learning
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Unveiling Berberine analogues as potential inhibitors of Escherichia coli FtsZ through machine learning molecular docking and molecular dynamics approach.

Scientific reports Apr 26, 2025
The bacterial cell division protein FtsZ, a crucial GTPase, plays a vital role in the formation of the contractile Z-ring, which is essential for bacterial cytokinesis. Consequently, inhibiting FtsZ could prevent the formation of proto-filaments and ...
Protein Binding Escherichia coli Machine Learning Bacterial Proteins Molecular Dynamics Simulation Cytoskeletal Proteins Anti-Bacterial Agents Hydrogen Bonding Berberine Molecular Docking Simulation
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Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network.

Cell Apr 23, 2025
In humans, selective and promiscuous interactions between 46 secreted chemokine ligands and 23 cell surface chemokine receptors of the G-protein-coupled receptor (GPCR) family form a complex network to coordinate cell migration. While chemokines and ...
Humans Protein Binding Ligands Chemokines Receptors, Chemokine Models, Molecular Amino Acid Sequence Receptors, G-Protein-Coupled
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