AIMC Topic: RNA-Binding Proteins

Clear Filters Showing 91 to 100 of 108 articles

ResidualBind: Uncovering Sequence-Structure Preferences of RNA-Binding Proteins with Deep Neural Networks.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2023
Deep neural networks have demonstrated improved performance at predicting sequence specificities of DNA- and RNA-binding proteins. However, it remains unclear why they perform better than previous methods that rely on k-mers and position weight matri...
Neural Networks, Computer DNA RNA Position-Specific Scoring Matrices Protein Binding RNA-Binding Proteins
View on PubMed DOI

PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning.

Bioinformatics (Oxford, England) Apr 12, 2022
MOTIVATION: Protein-RNA interactions play essential roles in many biological processes, including pre-mRNA processing, post-transcriptional gene regulation and RNA degradation. Accurate identification of binding sites on RNA-binding proteins (RBPs) i...
RNA Binding Sites RNA-Binding Proteins Membrane Proteins Protein Binding Deep Learning Computational Biology
View on PubMed DOI

Protein-RNA interaction prediction with deep learning: structure matters.

Briefings in bioinformatics Jan 17, 2022
Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Because of the limitation of the previous database, especially the lac...
Computational Biology RNA-Binding Proteins Protein Conformation Binding Sites RNA Algorithms Deep Learning
View on PubMed DOI

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...
Deep Learning Protein Binding Computational Biology Humans Neural Networks, Computer DNA DNA-Binding Proteins RNA RNA-Binding Proteins Proteome Intrinsically Disordered Proteins Nucleic Acids
View on PubMed DOI

EDCNN: identification of genome-wide RNA-binding proteins using evolutionary deep convolutional neural network.

Bioinformatics (Oxford, England) Jan 12, 2022
MOTIVATION: RNA-binding proteins (RBPs) are a group of proteins associated with RNA regulation and metabolism, and play an essential role in mediating the maturation, transport, localization and translation of RNA. Recently, Genome-wide RNA-binding e...
RNA-Binding Proteins RNA Neural Networks, Computer Software Algorithms
View on PubMed DOI

Prediction of RBP binding sites on circRNAs using an LSTM-based deep sequence learning architecture.

Briefings in bioinformatics Nov 5, 2021
Circular RNAs (circRNAs) are widely expressed in highly diverged eukaryotes. Although circRNAs have been known for many years, their function remains unclear. Interaction with RNA-binding protein (RBP) to influence post-transcriptional regulation is ...
Binding Sites RNA, Circular ROC Curve Computational Biology Databases, Genetic Base Sequence RNA-Binding Proteins Algorithms Reproducibility of Results Deep Learning
View on PubMed DOI

RNAProt: an efficient and feature-rich RNA binding protein binding site predictor.

GigaScience Aug 18, 2021
BACKGROUND: Cross-linking and immunoprecipitation followed by next-generation sequencing (CLIP-seq) is the state-of-the-art technique used to experimentally determine transcriptome-wide binding sites of RNA-binding proteins (RBPs). However, it relies...
Protein Binding RNA-Binding Proteins Neural Networks, Computer RNA Binding Sites
View on PubMed DOI

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...
Protein Conformation Neural Networks, Computer Binding Sites Software DNA DNA-Binding Proteins Protein Binding RNA RNA-Binding Proteins
View on PubMed DOI

RNA-binding protein recognition based on multi-view deep feature and multi-label learning.

Briefings in bioinformatics May 20, 2021
RNA-binding protein (RBP) is a class of proteins that bind to and accompany RNAs in regulating biological processes. An RBP may have multiple target RNAs, and its aberrant expression can cause multiple diseases. Methods have been designed to predict ...
Computational Biology RNA-Binding Proteins Neural Networks, Computer Machine Learning
View on PubMed DOI

Modeling multi-species RNA modification through multi-task curriculum learning.

Nucleic acids research Apr 19, 2021
N6-methyladenosine (m6A) is the most pervasive modification in eukaryotic mRNAs. Numerous biological processes are regulated by this critical post-transcriptional mark, such as gene expression, RNA stability, RNA structure and translation. Recently, ...
Adenosine Transcriptome RNA-Binding Proteins Datasets as Topic Databases, Genetic Software RNA Gene Expression Regulation Animals Humans Sequence Analysis, RNA Machine Learning
View on PubMed DOI
Popular Topics
Recent Journals