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DNA-Binding Proteins

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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...
Algorithms Reproducibility of Results Deep Learning Humans Neural Networks, Computer Internet DNA-Binding Proteins Binding Sites Protein Binding Computational Biology DNA
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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...
Time-Lapse Imaging Escherichia coli DNA-Binding Proteins Computer Simulation Machine Learning DNA Saccharomyces cerevisiae Protein Binding Algorithms Kinetics Single Molecule Imaging Computational Biology
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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...
Neural Networks, Computer Software Protein Binding RNA Protein Conformation Binding Sites RNA-Binding Proteins DNA DNA-Binding Proteins
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Machine Learning to Decode Genomics.

Clinical chemistry Jan 1, 2020
Databases, Factual Genomics DNA-Binding Proteins Humans Machine Learning
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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 ...
Gene Expression Regulation Binding Sites Humans Transcription Factors Regulatory Sequences, Nucleic Acid Algorithms Neural Networks, Computer Regulatory Elements, Transcriptional DNA Computational Biology DNA-Binding Proteins
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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...
Machine Learning Amino Acid Sequence Protein Conformation Binding Sites Sequence Analysis, Protein Databases, Protein Molecular Docking Simulation DNA Protein Binding DNA-Binding Proteins Computational Biology
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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-Binding Proteins Nucleic Acid Conformation Protein Array Analysis Binding Sites Nucleotide Motifs Support Vector Machine Sequence Analysis, DNA DNA Genomics Software Transcription Factors Protein Binding
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Correlation of Brain Neuropeptide (Nesfatin-1 and Orexin-A) Concentrations with Anthropometric and Biochemical Parameters in Malnourished Children.

Journal of clinical research in pediatric endocrinology Sep 1, 2015
OBJECTIVE: Malnutrition continues to be a leading cause of stunted growth in many countries. This study aimed to investigate serum nesfatin-1 and orexin-A levels in underweight children and the potential correlations of these levels with anthropometr...
Body Height Anthropometry Multivariate Analysis Child DNA-Binding Proteins Child Nutrition Disorders Nucleobindins Nerve Tissue Proteins Male Enzyme-Linked Immunosorbent Assay Body Weight Orexins Humans Thyrotropin Body Mass Index Case-Control Studies Vitamin B 12 Calcium-Binding Proteins Thyroxine Child, Preschool Female
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