AIMC Topic: DNA-Binding Proteins

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Divergence in a eukaryotic transcription factor's co-TF dependence involves multiple intrinsically disordered regions.

Nature communications Jun 18, 2025
Combinatorial control by transcription factors (TFs) is central to eukaryotic gene regulation, yet its mechanism, evolution, and regulatory impact are not well understood. Here we use natural variation in the yeast phosphate starvation (PHO) response...
Protein Binding Transcription Factors Saccharomyces cerevisiae Gene Expression Regulation, Fungal Candida glabrata Saccharomyces cerevisiae Proteins DNA-Binding Proteins Intrinsically Disordered Proteins Phosphates
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TET2 gene mutation status associated with poor prognosis of transition zone prostate cancer: a retrospective cohort study based on whole exome sequencing and machine learning models.

Frontiers in endocrinology Apr 14, 2025
BACKGROUND: Prostate cancer (PCa) in the transition zone (TZ) is uncommon and often poses challenges for early diagnosis, but its genomic determinants and therapeutic vulnerabilities remain poorly characterized.
Exome Sequencing Proto-Oncogene Proteins Dioxygenases Prognosis Prostatic Neoplasms Biomarkers, Tumor Humans Retrospective Studies Mutation Male Machine Learning Aged DNA-Binding Proteins Middle Aged
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TransBind allows precise detection of DNA-binding proteins and residues using language models and deep learning.

Communications biology Apr 5, 2025
Identifying DNA-binding proteins and their binding residues is critical for understanding diverse biological processes, but conventional experimental approaches are slow and costly. Existing machine learning methods, while faster, often lack accuracy...
Humans Software Sequence Alignment Sequence Analysis, Protein Deep Learning Computational Biology DNA-Binding Proteins
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Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model.

Cell genomics Apr 1, 2025
Signaling pathway components are well studied, but how they mediate cell-type-specific transcription responses is an unresolved problem. Using the Hippo pathway in mouse trophoblast stem cells as a model, we show that the DNA binding of signaling eff...
Animals TEA Domain Transcription Factors Muscle Proteins Hippo Signaling Pathway YAP-Signaling Proteins Adaptor Proteins, Signal Transducing Signal Transduction Phosphoproteins DNA-Binding Proteins Transcription Factors Trophoblasts Deep Learning Molecular Dynamics Simulation Protein Serine-Threonine Kinases Enhancer Elements, Genetic Protein Binding Mice
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Artificial intelligence-powered prediction of AIM-2 inflammasome sequences using transformers and graph attention networks in periodontal inflammation.

Scientific reports Mar 13, 2025
Periodontal inflammation is a chronic condition affecting the tissues surrounding teeth. Initiated by dental plaque, it triggers an immune response leading to tissue destruction. The AIM-2 inflammasome regulates this response, and understanding its p...
Inflammasomes Inflammation DNA-Binding Proteins Amino Acid Sequence Humans Artificial Intelligence
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Further Development of SAMPDI-3D: A Machine Learning Method for Predicting Binding Free Energy Changes Caused by Mutations in Either Protein or DNA.

Genes Jan 19, 2025
BACKGROUND/OBJECTIVES: Predicting the effects of protein and DNA mutations on the binding free energy of protein-DNA complexes is crucial for understanding how DNA variants impact wild-type cellular function. As many cellular interactions involve pro...
DNA Mutation DNA-Binding Proteins Humans Thermodynamics Machine Learning Protein Binding
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Computational staining of CD3/CD20 positive lymphocytes in human tissues with experimental confirmation in a genetically engineered mouse model.

Frontiers in immunology Oct 28, 2024
INTRODUCTION: Immune dysregulation plays a major role in cancer progression. The quantification of lymphocytic spatial inflammation may enable spatial system biology, improve understanding of therapeutic resistance, and contribute to prognostic imagi...
Mice, Knockout Antigens, CD20 DNA-Binding Proteins Mice Humans CD3 Complex Staining and Labeling Lymphocytes Animals Computational Biology Deep Learning
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DeepDBS: Identification of DNA-binding sites in protein sequences by using deep representations and random forest.

Methods (San Diego, Calif.) Sep 11, 2024
Interactions of biological molecules in organisms are considered to be primary factors for the lifecycle of that organism. Various important biological functions are dependent on such interactions and among different kinds of interactions, the protei...
Databases, Protein DNA Random Forest DNA-Binding Proteins Amino Acid Sequence Binding Sites Deep Learning Protein Binding Computational Biology Neural Networks, Computer Algorithms Sequence Analysis, Protein
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Deciphering the Language of Protein-DNA Interactions: A Deep Learning Approach Combining Contextual Embeddings and Multi-Scale Sequence Modeling.

Journal of molecular biology Aug 29, 2024
Deciphering the mechanisms governing protein-DNA interactions is crucial for understanding key cellular processes and disease pathways. In this work, we present a powerful deep learning approach that significantly advances the computational predictio...
DNA DNA-Binding Proteins Binding Sites Deep Learning Protein Binding Computational Biology Neural Networks, Computer
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Geometric deep learning of protein-DNA binding specificity.

Nature methods Aug 5, 2024
Predicting protein-DNA binding specificity is a challenging yet essential task for understanding gene regulation. Protein-DNA complexes usually exhibit binding to a selected DNA target site, whereas a protein binds, with varying degrees of binding sp...
Binding Sites DNA Models, Molecular Deep Learning DNA-Binding Proteins Protein Binding Computational Biology
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