AIMC Topic: DNA-Binding Proteins

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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...
Computational Biology Databases, Protein DNA Deep Learning Protein Binding Amino Acid Sequence Binding Sites Sequence Analysis, Protein Random Forest DNA-Binding Proteins Neural Networks, Computer Algorithms
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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...
Neural Networks, Computer Computational Biology DNA DNA-Binding Proteins Deep Learning Protein Binding Binding Sites
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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...
Models, Molecular DNA-Binding Proteins Binding Sites Protein Binding Computational Biology Deep Learning DNA
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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...
Databases, Protein DNA-Binding Proteins Neural Networks, Computer Computational Biology Humans
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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...
Computational Biology DNA Binding Sites DNA-Binding Proteins Algorithms Protein Binding Machine Learning
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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...
Thermodynamics Protein Binding Support Vector Machine DNA DNA-Binding Proteins Proteins Neural Networks, Computer Machine Learning Algorithms
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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...
Computational Biology RNA-Binding Proteins DNA DNA-Binding Proteins Databases, Protein Machine Learning Algorithms Protein Binding Humans RNA Binding Sites
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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 ...
DNA-Binding Proteins Algorithms Deep Learning Neural Networks, Computer Computational Biology Machine Learning
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DRBpred: A sequence-based machine learning method to effectively predict DNA- and RNA-binding residues.

Computers in biology and medicine Jan 29, 2024
DNA-binding and RNA-binding proteins are essential to an organism's normal life cycle. These proteins have diverse functions in various biological processes. DNA-binding proteins are crucial for DNA replication, transcription, repair, packaging, and ...
Machine Learning Databases, Protein Computational Biology DNA-Binding Proteins Algorithms RNA-Binding Proteins DNA Amino Acids RNA
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DBPboost:A method of classification of DNA-binding proteins based on improved differential evolution algorithm and feature extraction.

Methods (San Diego, Calif.) Jan 17, 2024
DNA-binding proteins are a class of proteins that can interact with DNA molecules through physical and chemical interactions. Their main functions include regulating gene expression, maintaining chromosome structure and stability, and more. DNA-bindi...
Support Vector Machine DNA DNA-Binding Proteins Algorithms Computational Biology
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