AIMC Topic: Binding Sites

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BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data.

Nucleic acids research Jan 6, 2025
BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, trai...
Proteins Databases, Protein Internet Humans Protein Binding Knowledge Bases Binding Sites Small Molecule Libraries
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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...
DNA-Binding Proteins Software Binding Sites Algorithms Graph Neural Networks Neural Networks, Computer Protein Binding Computational Biology Databases, Protein DNA
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Machine and Deep Learning Methods for Predicting 3D Genome Organization.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2025
Three-dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, topologically associating domains (TADs), and A/B compartments, play critical roles in a wide range of cellular processes by regulating gene expressi...
Deep Learning Enhancer Elements, Genetic Genomics Chromatin Humans Promoter Regions, Genetic Computational Biology Machine Learning Binding Sites Software Genome
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Improving generalizability of drug-target binding prediction by pre-trained multi-view molecular representations.

Bioinformatics (Oxford, England) Dec 26, 2024
MOTIVATION: Most drugs start on their journey inside the body by binding the right target proteins. This is the reason that numerous efforts have been devoted to predicting the drug-target binding during drug development. However, the inherent divers...
Protein Binding Computational Biology Proteins Humans Neural Networks, Computer Drug Discovery Binding Sites
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Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.

Briefings in bioinformatics Sep 23, 2024
Transcriptional factors (TFs) in bacteria play a crucial role in gene regulation by binding to specific DNA sequences, thereby assisting in the activation or repression of genes. Despite their central role, deciphering shape recognition of bacterial ...
Machine Learning Bacterial Proteins Algorithms Nucleic Acid Conformation Protein Binding DNA, Bacterial Binding Sites Bacteria Transcription Factors Computational Biology DNA
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MLSNet: a deep learning model for predicting transcription factor binding sites.

Briefings in bioinformatics Sep 23, 2024
Accurate prediction of transcription factor binding sites (TFBSs) is essential for understanding gene regulation mechanisms and the etiology of diseases. Despite numerous advances in deep learning for predicting TFBSs, their performance can still be ...
DNA Binding Sites Chromatin Immunoprecipitation Sequencing Computational Biology Humans Transcription Factors Algorithms Deep Learning
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An integrated machine-learning model to predict nucleosome architecture.

Nucleic acids research Sep 23, 2024
We demonstrate that nucleosomes placed in the gene body can be accurately located from signal decay theory assuming two emitters located at the beginning and at the end of genes. These generated wave signals can be in phase (leading to well defined n...
Humans Machine Learning Transcription Factors DNA Binding Sites Nucleosomes
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Machine learning enables pan-cancer identification of mutational hotspots at persistent CTCF binding sites.

Nucleic acids research Aug 12, 2024
CCCTC-binding factor (CTCF) is an insulator protein that binds to a highly conserved DNA motif and facilitates regulation of three-dimensional (3D) nuclear architecture and transcription. CTCF binding sites (CTCF-BSs) reside in non-coding DNA and are...
Mutation Binding Sites Chromatin CCCTC-Binding Factor Neoplasms Protein Binding Prostatic Neoplasms Breast Neoplasms Male Humans Machine Learning Female
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BertSNR: an interpretable deep learning framework for single-nucleotide resolution identification of transcription factor binding sites based on DNA language model.

Bioinformatics (Oxford, England) Aug 2, 2024
MOTIVATION: Transcription factors are pivotal in the regulation of gene expression, and accurate identification of transcription factor binding sites (TFBSs) at high resolution is crucial for understanding the mechanisms underlying gene regulation. T...
Deep Learning Computational Biology Software Transcription Factors Sequence Analysis, DNA Algorithms DNA Binding Sites
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Machine learning-assisted substrate binding pocket engineering based on structural information.

Briefings in bioinformatics Jul 25, 2024
Engineering enzyme-substrate binding pockets is the most efficient approach for modifying catalytic activity, but is limited if the substrate binding sites are indistinct. Here, we developed a 3D convolutional neural network for predicting protein-li...
Acid Phosphatase Ligands Protein Binding Neural Networks, Computer Klebsiella Models, Molecular Substrate Specificity Machine Learning Binding Sites Bacterial Proteins Protein Engineering Bacillus anthracis
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