AIMC Topic: DNA-Binding Proteins

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Development of a Machine Learning Model Using Limited Features to Predict 6-Month Mortality at Treatment Decision Points for Patients With Advanced Solid Tumors.

JCO clinical cancer informatics Mar 1, 2022
PURPOSE: Patients with advanced solid tumors may receive intensive treatments near the end of life. This study aimed to create a machine learning (ML) model using limited features to predict 6-month mortality at treatment decision points (TDPs).
Adult Neoplasms Predictive Value of Tests DNA-Binding Proteins Humans Machine Learning Prognosis
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Detection of transcription factors binding to methylated DNA by deep recurrent neural network.

Briefings in bioinformatics Jan 17, 2022
Transcription factors (TFs) are proteins specifically involved in gene expression regulation. It is generally accepted in epigenetics that methylated nucleotides could prevent the TFs from binding to DNA fragments. However, recent studies have confir...
Humans Neural Networks, Computer Algorithms Deep Learning Binding Sites DNA DNA-Binding Proteins Gene Expression Regulation Protein Binding Transcription Factors DNA Methylation
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DeepDISOBind: accurate prediction of RNA-, DNA- and protein-binding intrinsically disordered residues with deep multi-task learning.

Briefings in bioinformatics Jan 17, 2022
Proteins with intrinsically disordered regions (IDRs) are common among eukaryotes. Many IDRs interact with nucleic acids and proteins. Annotation of these interactions is supported by computational predictors, but to date, only one tool that predicts...
RNA Intrinsically Disordered Proteins Nucleic Acids Proteome DNA DNA-Binding Proteins Humans Neural Networks, Computer Computational Biology RNA-Binding Proteins Deep Learning Protein Binding
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SAResNet: self-attention residual network for predicting DNA-protein binding.

Briefings in bioinformatics Sep 2, 2021
Knowledge of the specificity of DNA-protein binding is crucial for understanding the mechanisms of gene expression, regulation and gene therapy. In recent years, deep-learning-based methods for predicting DNA-protein binding from sequence data have a...
Protein Binding Computational Biology DNA Algorithms Reproducibility of Results Deep Learning Internet DNA-Binding Proteins Binding Sites Humans Neural Networks, Computer
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Bound2Learn: a machine learning approach for classification of DNA-bound proteins from single-molecule tracking experiments.

Nucleic acids research Aug 20, 2021
DNA-bound proteins are essential elements for the maintenance, regulation, and use of the genome. The time they spend bound to DNA provides useful information on their stability within protein complexes and insight into the understanding of biologica...
DNA-Binding Proteins Saccharomyces cerevisiae Single Molecule Imaging Time-Lapse Imaging Escherichia coli DNA Kinetics Computer Simulation Protein Binding Computational Biology Machine Learning Algorithms
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GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues.

Nucleic acids research May 21, 2021
Knowledge of the interactions between proteins and nucleic acids is the basis of understanding various biological activities and designing new drugs. How to accurately identify the nucleic-acid-binding residues remains a challenging task. In this pap...
DNA DNA-Binding Proteins RNA Software Protein Conformation Neural Networks, Computer Protein Binding Binding Sites RNA-Binding Proteins
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Machine Learning to Decode Genomics.

Clinical chemistry Jan 1, 2020
Humans Machine Learning Databases, Factual Genomics DNA-Binding Proteins
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DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants.

Nucleic acids research Jun 20, 2018
The complex system of gene expression is regulated by the cell type-specific binding of transcription factors (TFs) to regulatory elements. Identifying variants that disrupt TF binding and lead to human diseases remains a great challenge. To address ...
Binding Sites Regulatory Elements, Transcriptional Regulatory Sequences, Nucleic Acid Humans DNA Neural Networks, Computer DNA-Binding Proteins Gene Expression Regulation Algorithms Computational Biology Transcription Factors
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Survey of Computational Approaches for Prediction of DNA-Binding Residues on Protein Surfaces.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2018
The increasing number of protein structures with uncharacterized function necessitates the development of in silico prediction methods for functional annotations on proteins. In this chapter, different kinds of computational approaches are briefly in...
Computational Biology Databases, Protein DNA-Binding Proteins Binding Sites DNA Machine Learning Amino Acid Sequence Sequence Analysis, Protein Molecular Docking Simulation Protein Conformation Protein Binding
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DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.

Bioinformatics (Oxford, England) Oct 1, 2017
MOTIVATION: Transcription factors (TFs) bind to specific DNA sequence motifs. Several lines of evidence suggest that TF-DNA binding is mediated in part by properties of the local DNA shape: the width of the minor groove, the relative orientations of ...
DNA Transcription Factors Software DNA-Binding Proteins Support Vector Machine Protein Binding Protein Array Analysis Nucleic Acid Conformation Sequence Analysis, DNA Genomics Binding Sites Nucleotide Motifs
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