AIMC Topic: DNA-Binding Proteins

Clear Filters Showing 11 to 20 of 107 articles

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...
Humans Mutation DNA-Binding Proteins Thermodynamics Protein Binding DNA Machine Learning
View on PubMed DOI

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...
Computational Biology CD3 Complex Lymphocytes Deep Learning Mice, Knockout Mice DNA-Binding Proteins Humans Staining and Labeling Animals Antigens, CD20
View on PubMed DOI

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...
Binding Sites Sequence Analysis, Protein DNA-Binding Proteins Amino Acid Sequence Protein Binding Algorithms Databases, Protein Neural Networks, Computer Computational Biology Deep Learning DNA Random Forest
View on PubMed DOI

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 Protein Binding Computational Biology Neural Networks, Computer Deep Learning
View on PubMed DOI

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...
Computational Biology DNA Models, Molecular Deep Learning Protein Binding DNA-Binding Proteins Binding Sites
View on PubMed DOI

PreDBP-PLMs: Prediction of DNA-binding proteins based on pre-trained protein language models and convolutional neural networks.

Analytical biochemistry Jul 8, 2024
The recognition of DNA-binding proteins (DBPs) is the crucial step to understanding their roles in various biological processes such as genetic regulation, gene expression, cell cycle control, DNA repair, and replication within cells. However, conven...
Computational Biology Databases, Protein DNA-Binding Proteins Humans Neural Networks, Computer
View on PubMed DOI

Prediction of Protein-DNA Interface Hot Spots Based on Empirical Mode Decomposition and Machine Learning.

Genes May 23, 2024
Protein-DNA complex interactivity plays a crucial role in biological activities such as gene expression, modification, replication and transcription. Understanding the physiological significance of protein-DNA binding interfacial hot spots, as well a...
Binding Sites DNA DNA-Binding Proteins Machine Learning Protein Binding Computational Biology Algorithms
View on PubMed DOI

ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein-DNA Interaction Hotspots.

Journal of chemical information and modeling Apr 8, 2024
Protein-DNA interactions are pivotal to various cellular processes. Precise identification of the hotspot residues for protein-DNA interactions holds great significance for revealing the intricate mechanisms in protein-DNA recognition and for providi...
Neural Networks, Computer Machine Learning Thermodynamics Support Vector Machine DNA-Binding Proteins Proteins Algorithms DNA Protein Binding
View on PubMed DOI

EPDRNA: A Model for Identifying DNA-RNA Binding Sites in Disease-Related Proteins.

The protein journal Mar 16, 2024
Protein-DNA and protein-RNA interactions are involved in many biological processes and regulate many cellular functions. Moreover, they are related to many human diseases. To understand the molecular mechanism of protein-DNA binding and protein-RNA b...
DNA-Binding Proteins RNA Binding Sites RNA-Binding Proteins Databases, Protein Protein Binding DNA Humans Computational Biology Machine Learning Algorithms
View on PubMed DOI

Deep-WET: a deep learning-based approach for predicting DNA-binding proteins using word embedding techniques with weighted features.

Scientific reports Feb 5, 2024
DNA-binding proteins (DBPs) play a significant role in all phases of genetic processes, including DNA recombination, repair, and modification. They are often utilized in drug discovery as fundamental elements of steroids, antibiotics, and anticancer ...
Machine Learning Algorithms Deep Learning Neural Networks, Computer Computational Biology DNA-Binding Proteins
View on PubMed DOI
Popular Topics
Recent Journals