AIMC Topic: DNA-Binding Proteins

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DRBP-EDP: classification of DNA-binding proteins and RNA-binding proteins using ESM-2 and dual-path neural network.

NAR genomics and bioinformatics Jun 1, 2025
Regulation of DNA or RNA at the transcriptional, post-transcriptional, and translational levels are key steps in the central dogma of molecular biology. DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs) play pivotal roles in the precise reg...
Humans Neural Networks, Computer RNA-Binding Proteins Databases, Protein DNA-Binding Proteins Software Deep Learning
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PLM-DBPs: enhancing plant DNA-binding protein prediction by integrating sequence-based and structure-aware protein language models.

Briefings in bioinformatics May 1, 2025
DNA-binding proteins (DBPs) play a crucial role in gene regulation, development, and environmental responses across plants, animals, and microorganisms. Existing DBP prediction methods are largely limited to sequence information, whether through hand...
Plant Proteins DNA-Binding Proteins Plants Deep Learning Computational Biology
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iProtDNA-SMOTE: Enhancing protein-DNA binding sites prediction through imbalanced graph neural networks.

PloS one Jan 1, 2025
Protein-DNA interactions play a crucial role in cellular biology, essential for maintaining life processes and regulating cellular functions. We propose a method called iProtDNA-SMOTE, which utilizes non-equilibrium graph neural networks along with p...
Neural Networks, Computer Software Algorithms DNA-Binding Proteins Databases, Protein Graph Neural Networks Protein Binding DNA Binding Sites Computational Biology
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Screening of gastric cancer diagnostic biomarkers in the homologous recombination signaling pathway and assessment of their clinical and radiomic correlations.

Cancer medicine Aug 1, 2024
BACKGROUND: Homologous recombination plays a vital role in the occurrence and drug resistance of gastric cancer. This study aimed to screen new gastric cancer diagnostic biomarkers in the homologous recombination pathway and then used radiomic featur...
Signal Transduction Neoplasm Staging Middle Aged Gene Expression Regulation, Neoplastic DNA-Binding Proteins Homologous Recombination Aged Stomach Neoplasms Biomarkers, Tumor Male Radiomics Tomography, X-Ray Computed Female Humans Machine Learning
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ProkDBP: Toward more precise identification of prokaryotic DNA binding proteins.

Protein science : a publication of the Protein Society Jun 1, 2024
Prokaryotic DNA binding proteins (DBPs) play pivotal roles in governing gene regulation, DNA replication, and various cellular functions. Accurate computational models for predicting prokaryotic DBPs hold immense promise in accelerating the discovery...
Machine Learning Algorithms Bacterial Proteins DNA-Binding Proteins Computational Biology
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EGPDI: identifying protein-DNA binding sites based on multi-view graph embedding fusion.

Briefings in bioinformatics May 23, 2024
Mechanisms of protein-DNA interactions are involved in a wide range of biological activities and processes. Accurately identifying binding sites between proteins and DNA is crucial for analyzing genetic material, exploring protein functions, and desi...
DNA DNA-Binding Proteins Binding Sites Neural Networks, Computer Protein Binding Algorithms Computational Biology
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Improved prediction of DNA and RNA binding proteins with deep learning models.

Briefings in bioinformatics May 23, 2024
Nucleic acid-binding proteins (NABPs), including DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs), play important roles in essential biological processes. To facilitate functional annotation and accurate prediction of different types of NA...
Humans Neural Networks, Computer RNA-Binding Proteins DNA-Binding Proteins Deep Learning Computational Biology
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Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling.

Briefings in bioinformatics Mar 19, 2023
Recognizing binding sites of DNA-binding proteins is a key factor for elucidating transcriptional regulation in organisms. ChIP-exo enables researchers to delineate genome-wide binding landscapes of DNA-binding proteins with near single base-pair res...
Algorithms Deep Learning Software Binding Sites Chromatin Immunoprecipitation Sequence Analysis, DNA Chromatin Immunoprecipitation Sequencing DNA-Binding Proteins
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A deep learning-based method for the prediction of DNA interacting residues in a protein.

Briefings in bioinformatics Sep 20, 2022
DNA-protein interaction is one of the most crucial interactions in the biological system, which decides the fate of many processes such as transcription, regulation and splicing of genes. In this study, we trained our models on a training dataset of ...
Position-Specific Scoring Matrices Deep Learning DNA Databases, Protein DNA-Binding Proteins
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DNA-binding protein prediction based on deep transfer learning.

Mathematical biosciences and engineering : MBE May 24, 2022
The study of DNA binding proteins (DBPs) is of great importance in the biomedical field and plays a key role in this field. At present, many researchers are working on the prediction and detection of DBPs. Traditional DBP prediction mainly uses machi...
DNA-Binding Proteins Machine Learning Algorithms Humans Neural Networks, Computer
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