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Binding Sites

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Prediction of Transcription Factor Binding Sites With an Attention Augmented Convolutional Neural Network.

IEEE/ACM transactions on computational biology and bioinformatics Dec 8, 2022
Identification of transcription factor binding sites (TFBSs) is essential for revealing the rules of protein-DNA binding. Although some computational methods have been presented to predict TFBSs using epigenomic and sequence features, most of them ig...
Neural Networks, Computer Transcription Factors Binding Sites Algorithms Protein Binding
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Classification of Protein-Binding Sites Using a Spherical Convolutional Neural Network.

Journal of chemical information and modeling Nov 7, 2022
The analysis and comparison of protein-binding sites aid various applications in the drug discovery process, e.g., hit finding, drug repurposing, and polypharmacology. Classification of binding sites has been a hot topic for the past 30 years, and ma...
Binding Sites Protein Binding Proteins Neural Networks, Computer Machine Learning
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Predicting Conserved Water Molecules in Binding Sites of Proteins Using Machine Learning Methods and Combining Features.

Computational and mathematical methods in medicine Oct 3, 2022
Water molecules play an important role in many biological processes in terms of stabilizing protein structures, assisting protein folding, and improving binding affinity. It is well known that, due to the impacts of various environmental factors, it ...
Binding Sites Support Vector Machine Bayes Theorem Machine Learning Humans Solvents Proteins Water
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TAMC: A deep-learning approach to predict motif-centric transcriptional factor binding activity based on ATAC-seq profile.

PLoS computational biology Sep 12, 2022
Determining transcriptional factor binding sites (TFBSs) is critical for understanding the molecular mechanisms regulating gene expression in different biological conditions. Biological assays designed to directly mapping TFBSs require large sample s...
Binding Sites Protein Binding Chromatin Immunoprecipitation Sequencing Transcription Factors Deep Learning
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Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning.

Journal of chemical information and modeling Aug 30, 2022
The mechanism of transcriptional activation/repression of the nuclear receptors (NRs) involves two main conformations of the NR protein, namely, the active (agonistic) and inactive (antagonistic) conformations. Binding of agonists or antagonists to t...
Receptors, Cytoplasmic and Nuclear Binding Sites Machine Learning Ligands
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Deep Learning-Based Label-Free Surface-Enhanced Raman Scattering Screening and Recognition of Small-Molecule Binding Sites in Proteins.

Analytical chemistry Aug 15, 2022
Identification of small-molecule binding sites in proteins is of great significance in analysis of protein function and drug design. Modified sites can be recognized via proteolytic cleavage followed by liquid chromatography-mass spectrometry (LC-MS)...
Peptides Deep Learning Tandem Mass Spectrometry Binding Sites Spectrum Analysis, Raman Proteins
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iDRBP-ECHF: Identifying DNA- and RNA-binding proteins based on extensible cubic hybrid framework.

Computers in biology and medicine Aug 13, 2022
Proteins interact with nucleic acids to regulate the life activities of organisms. Therefore, how to accurately and efficiently identify nucleic acid-binding proteins (NABPs) is particularly significant. Some sequence-based computational methods have...
DNA-Binding Proteins Binding Sites Machine Learning Computational Biology RNA-Binding Proteins Algorithms DNA
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Predicting RBP Binding Sites of RNA With High-Order Encoding Features and CNN-BLSTM Hybrid Model.

IEEE/ACM transactions on computational biology and bioinformatics Aug 8, 2022
RNA binding protein (RBP) is extensively involved in various cellular regulatory processes through the interaction with RNAs. Capturing the RBP binding preferences is fundamental for revealing the pathogenesis of complex diseases. Many experimental d...
RNA Binding Sites Protein Binding Neural Networks, Computer RNA-Binding Proteins
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GraphSite: Ligand Binding Site Classification with Deep Graph Learning.

Biomolecules Jul 29, 2022
The binding of small organic molecules to protein targets is fundamental to a wide array of cellular functions. It is also routinely exploited to develop new therapeutic strategies against a variety of diseases. On that account, the ability to effect...
Neural Networks, Computer Ligands Molecular Docking Simulation Artificial Intelligence Binding Sites Proteins
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Prediction of protein mononucleotide binding sites using AlphaFold2 and machine learning.

Computational biology and chemistry Jul 23, 2022
In this study, we developed a system that predicts the binding sites of proteins for five mononucleotides (AMP, ADP, ATP, GDP, and GTP). The system comprises two machine learning (ML)-based predictors using a convolutional neural network and a gradie...
Adenosine Triphosphate Ligands Binding Sites Adenosine Diphosphate Protein Binding Proteins Machine Learning Adenosine Monophosphate
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