AIMC Topic: DNA-Binding Proteins

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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 ...
Humans DNA-Binding Proteins Computational Biology Protein Conformation Proteome DNA Binding Sites Software Animals Deep Learning
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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...
Male DNA-Binding Proteins Disease Progression Humans Alzheimer Disease Female Algorithms tau Proteins Aged Brain Cognitive Dysfunction Aged, 80 and over Deep Learning Cognition Phosphorylation
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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...
Machine Learning DNA-Binding Proteins Ubiquitin-Protein Ligases Humans 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...
Algorithms Binding Sites Position-Specific Scoring Matrices Support Vector Machine Databases, Protein DNA-Binding Proteins
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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...
Genome Chromatin Gene Expression Regulation Histones Binding Sites Humans Neural Networks, Computer Protein Binding Transcription Factors Basic Helix-Loop-Helix Transcription Factors DNA-Binding Proteins
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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...
Gene Expression Regulation Genome, Human Cell Cycle Proteins CCCTC-Binding Factor Chromosomal Proteins, Non-Histone Models, Genetic Cohesins Humans Sequence Analysis, DNA Neural Networks, Computer DNA-Binding Proteins
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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...
Machine Learning Protein Binding Computational Biology RNA-Binding Proteins DNA-Binding Proteins Binding Sites Humans RNA Neural Networks, Computer
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Use Chou's 5-Step Rule to Predict DNA-Binding Proteins with Evolutionary Information.

BioMed research international Jul 27, 2020
The knowledge of DNA-binding proteins would help to understand the functions of proteins better in cellular biological processes. Research on the prediction of DNA-binding proteins can promote the research of drug proteins and computer acidified drug...
Evolution, Molecular Databases, Protein DNA-Binding Proteins Computational Biology Support Vector Machine
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Clinical-Grade Detection of Microsatellite Instability in Colorectal Tumors by Deep Learning.

Gastroenterology Jun 17, 2020
BACKGROUND & AIMS: Microsatellite instability (MSI) and mismatch-repair deficiency (dMMR) in colorectal tumors are used to select treatment for patients. Deep learning can detect MSI and dMMR in tumor samples on routine histology slides faster and le...
MutS Homolog 2 Protein Male Middle Aged Deep Learning Humans Adult Neoplastic Syndromes, Hereditary Female Colorectal Neoplasms Mismatch Repair Endonuclease PMS2 Microsatellite Instability Brain Neoplasms Cohort Studies DNA-Binding Proteins ROC Curve MutL Protein Homolog 1 Predictive Value of Tests
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PredDBP-Stack: Prediction of DNA-Binding Proteins from HMM Profiles using a Stacked Ensemble Method.

BioMed research international Apr 13, 2020
DNA-binding proteins (DBPs) play vital roles in all aspects of genetic activities. However, the identification of DBPs by using wet-lab experimental approaches is often time-consuming and laborious. In this study, we develop a novel computational met...
Software Support Vector Machine DNA-Binding Proteins Databases, Protein
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