AIMC Topic: DNA-Binding Proteins

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DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning.

Journal of bioinformatics and computational biology Jul 21, 2021
DNA-binding proteins (DBPs) perform an influential role in diverse biological activities like DNA replication, slicing, repair, and transcription. Some DBPs are indispensable for understanding many types of human cancers (i.e. lung, breast, and liver...
Humans Algorithms DNA-Binding Proteins Amino Acid Sequence Position-Specific Scoring Matrices Computational Biology Support Vector Machine Databases, Protein
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A sequence-based multiple kernel model for identifying DNA-binding proteins.

BMC bioinformatics May 31, 2021
BACKGROUND: DNA-Binding Proteins (DBP) plays a pivotal role in biological system. A mounting number of researchers are studying the mechanism and detection methods. To detect DBP, the tradition experimental method is time-consuming and resource-consu...
Machine Learning Support Vector Machine DNA-Binding Proteins
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DeepD2V: A Novel Deep Learning-Based Framework for Predicting Transcription Factor Binding Sites from Combined DNA Sequence.

International journal of molecular sciences May 24, 2021
Predicting in vivo protein-DNA binding sites is a challenging but pressing task in a variety of fields like drug design and development. Most promoters contain a number of transcription factor (TF) binding sites, but only a small minority has been id...
DNA-Binding Proteins Promoter Regions, Genetic K562 Cells Binding Sites Transcription Factors Cell Line DNA Deep Learning Computational Biology Humans Software
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DeepDISE: DNA Binding Site Prediction Using a Deep Learning Method.

International journal of molecular sciences May 24, 2021
It is essential for future research to develop a new, reliable prediction method of DNA binding sites because DNA binding sites on DNA-binding proteins provide critical clues about protein function and drug discovery. However, the current prediction ...
Computational Biology Proteome DNA Animals Deep Learning DNA-Binding Proteins Protein Conformation Binding Sites Humans Software
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Application of deep learning to understand resilience to Alzheimer's disease pathology.

Brain pathology (Zurich, Switzerland) May 19, 2021
People who have Alzheimer's disease neuropathologic change (ADNC) typically associated with dementia but not the associated cognitive decline can be considered to be "resilient" to the effects of ADNC. We have previously reported lower neocortical le...
tau Proteins Phosphorylation DNA-Binding Proteins Alzheimer Disease Brain Female Aged Humans Deep Learning Aged, 80 and over Algorithms Cognitive Dysfunction Male Cognition Disease Progression
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Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients.

Nature cancer Jan 25, 2021
Cell-line screens create expansive datasets for learning predictive markers of drug response, but these models do not readily translate to the clinic with its diverse contexts and limited data. In the present study, we apply a recently developed tech...
Ubiquitin-Protein Ligases Machine Learning Humans DNA-Binding Proteins Neural Networks, Computer
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TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features.

Journal of chemical information and modeling Jan 7, 2021
Protein-DNA interactions exist ubiquitously and play important roles in the life cycles of living cells. The accurate identification of DNA-binding proteins (DBPs) is one of the key steps to understand the mechanisms of protein-DNA interactions. Alth...
Databases, Protein Position-Specific Scoring Matrices DNA-Binding Proteins Algorithms Binding Sites Support Vector Machine
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An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding.

Genome biology Jan 7, 2021
BACKGROUND: Transcription factor (TF) binding specificity is determined via a complex interplay between the transcription factor's DNA binding preference and cell type-specific chromatin environments. The chromatin features that correlate with transc...
Protein Binding Transcription Factors Basic Helix-Loop-Helix Transcription Factors DNA-Binding Proteins Gene Expression Regulation Humans Chromatin Histones Binding Sites Neural Networks, Computer Genome
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Predicting 3D genome folding from DNA sequence with Akita.

Nature methods Oct 12, 2020
In interphase, the human genome sequence folds in three dimensions into a rich variety of locus-specific contact patterns. Cohesin and CTCF (CCCTC-binding factor) are key regulators; perturbing the levels of either greatly disrupts genome-wide foldin...
DNA-Binding Proteins Gene Expression Regulation Genome, Human Models, Genetic Cohesins Cell Cycle Proteins Humans Sequence Analysis, DNA CCCTC-Binding Factor Neural Networks, Computer Chromosomal Proteins, Non-Histone
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iDRBP_MMC: Identifying DNA-Binding Proteins and RNA-Binding Proteins Based on Multi-Label Learning Model and Motif-Based Convolutional Neural Network.

Journal of molecular biology Sep 11, 2020
DNA-binding protein (DBP) and RNA-binding protein (RBP) are playing crucial roles in gene expression. Accurate identification of them is of great significance, and accurately computational predictors are highly required. In previous studies, DBP reco...
RNA-Binding Proteins Machine Learning Binding Sites DNA-Binding Proteins Humans Protein Binding RNA Neural Networks, Computer Computational Biology
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