AIMC Topic: Binding Sites

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Deep learning for de-convolution of Smad2 versus Smad3 binding sites.

BMC genomics Jul 20, 2022
BACKGROUND: The transforming growth factor beta-1 (TGF β-1) cytokine exerts both pro-tumor and anti-tumor effects in carcinogenesis. An increasing body of literature suggests that TGF β-1 signaling outcome is partially dependent on the regulatory tar...
Smad3 Protein Binding Sites Transforming Growth Factor beta Smad2 Protein Deep Learning Signal Transduction Cell Line
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Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications.

International journal of molecular sciences Jul 12, 2022
All living organisms require metal ions for their energy production and metabolic and biosynthetic processes. Within cells, the metal ions involved in the formation of adducts interact with metabolites and macromolecules (proteins and nucleic acids)....
Metalloproteins Databases, Protein Binding Sites Computational Biology Deep Learning Metals
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A web server for identifying circRNA-RBP variable-length binding sites based on stacked generalization ensemble deep learning network.

Methods (San Diego, Calif.) Jul 8, 2022
Circular RNA (circRNA) can exert biological functions by interacting with RNA-binding protein (RBP), and some deep learning-based methods have been developed to predict RBP binding sites on circRNA. However, most of these methods identify circRNA-RBP...
RNA, Circular RNA-Binding Proteins Algorithms Binding Sites Deep Learning
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ProB-Site: Protein Binding Site Prediction Using Local Features.

Cells Jul 5, 2022
Protein-protein interactions (PPIs) are responsible for various essential biological processes. This information can help develop a new drug against diseases. Various experimental methods have been employed for this purpose; however, their applicatio...
Neural Networks, Computer Amino Acids Binding Sites Protein Binding Proteins
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AI-based prediction of new binding site and virtual screening for the discovery of novel P2X3 receptor antagonists.

European journal of medicinal chemistry Jul 1, 2022
Artificial intelligence (AI) has been recognized as a powerful technique that can accelerate drug discovery during the hit compound identification step. However, most simple deep learning models have been used for naive pre-filtering as the predictio...
Molecular Docking Simulation Drug Discovery Artificial Intelligence Binding Sites Purinergic P2X Receptor Antagonists Molecular Dynamics Simulation Ligands Protein Binding
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DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites.

BMC bioinformatics Jun 29, 2022
BACKGROUND: Addressing the laborious nature of traditional biological experiments by using an efficient computational approach to analyze RNA-binding proteins (RBPs) binding sites has always been a challenging task. RBPs play a vital role in post-tra...
RNA Binding Sites Protein Binding RNA-Binding Proteins Neural Networks, Computer
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Explainable deep drug-target representations for binding affinity prediction.

BMC bioinformatics Jun 17, 2022
BACKGROUND: Several computational advances have been achieved in the drug discovery field, promoting the identification of novel drug-target interactions and new leads. However, most of these methodologies have been overlooking the importance of prov...
Proteins Binding Sites Plant Extracts Neural Networks, Computer Reproducibility of Results
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Machine Learning Guided Batched Design of a Bacterial Ribosome Binding Site.

ACS synthetic biology Jun 15, 2022
Optimization of gene expression levels is an essential part of the organism design process. Fine control of this process can be achieved by engineering transcription and translation control elements, including the ribosome binding site (RBS). Unfortu...
Binding Sites Ribosomes Machine Learning Algorithms
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Characterizing collaborative transcription regulation with a graph-based deep learning approach.

PLoS computational biology Jun 6, 2022
Human epigenome and transcription activities have been characterized by a number of sequence-based deep learning approaches which only utilize the DNA sequences. However, transcription factors interact with each other, and their collaborative regulat...
Transcription Factors DNA Gene Expression Regulation Binding Sites Deep Learning Protein Binding Humans Chromatin
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Translating from Proteins to Ribonucleic Acids for Ligand-binding Site Detection.

Molecular informatics Jun 1, 2022
Identifying druggable ligand-binding sites on the surface of the macromolecular targets is an important process in structure-based drug discovery. Deep-learning models have been shown to successfully predict ligand-binding sites of proteins. As a ste...
Ligands Proteins Binding Sites RNA Neural Networks, Computer
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