Protein–DNA/RNA interactions: Machine intelligence tools and approaches in the era of artificial intelligence and big data
Sign Up to like & getrecommendations! Published in 2022 at "PROTEOMICS"
DOI: 10.1002/pmic.202100197
Abstract: With the development of artificial intelligence (AI) technologies and the availability of large amounts of biological data, computational methods for proteomics have undergone a developmental process from traditional machine learning to deep learning. This review… read more here.
Keywords: intelligence; machine; artificial intelligence; rna interactions ... See more keywords
Computational methods for predicting hotspots at protein–RNA interfaces
Sign Up to like & getrecommendations! Published in 2021 at "Wiley Interdisciplinary Reviews: RNA"
DOI: 10.1002/wrna.1675
Abstract: Protein–RNA interactions play essential roles in many critical biological events. A comprehensive understanding of the mechanisms underlying these interactions is helpful when studying cellular activities and therapeutic applications. Hotspots are a small portion of residues… read more here.
Keywords: computational methods; predicting hotspots; hotspots protein; rna interactions ... See more keywords
Detecting RNA–RNA interactome
Sign Up to like & getrecommendations! Published in 2022 at "Wiley Interdisciplinary Reviews: RNA"
DOI: 10.1002/wrna.1715
Abstract: The last decade has seen a robust increase in various types of novel RNA molecules and their complexity in gene regulation. RNA molecules play a critical role in cellular events by interacting with other biomolecules,… read more here.
Keywords: rna interactome; rna molecules; rna; detecting rna ... See more keywords
Using Native RIP, UV-CLIP or fCLIP to Address Protein-RNA Interactions In Vivo.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1386-3_9
Abstract: Stable and transient interactions between molecules are determinant for cell function. Among those, numerous proteins contact coding and noncoding RNAs to modulate their fate and promote their activity. The identification of such interactions as well… read more here.
Keywords: rna interactions; native rip; rip; rip clip ... See more keywords
Free energy calculations of RNA interactions.
Sign Up to like & getrecommendations! Published in 2019 at "Methods"
DOI: 10.1016/j.ymeth.2019.02.014
Abstract: This review discusses the use of molecular dynamics free energy calculations for characterizing RNA interactions, with particular emphasis on molecular recognition events involved in mRNA translation on the ribosome. The general methodology for efficient free… read more here.
Keywords: methodology; energy calculations; energy; rna interactions ... See more keywords
RNA helicases regulate RNA condensates
Sign Up to like & getrecommendations! Published in 2020 at "Cell Research"
DOI: 10.1038/s41422-020-0296-7
Abstract: Stress granules are cytoplasmic membraneless RNA condensates for storing non-translating mRNAs, which are induced in response to various forms of stress. In a recent issue of Cell, Tauber et al. show that RNA helicases, particularly… read more here.
Keywords: rna rna; rna; rna interactions; formation ... See more keywords
Global in situ profiling of RNA-RNA spatial interactions with RIC-seq.
Sign Up to like & getrecommendations! Published in 2021 at "Nature protocols"
DOI: 10.1038/s41596-021-00524-2
Abstract: Emerging evidence has demonstrated that RNA-RNA interactions are vital in controlling diverse biological processes, including transcription, RNA splicing and protein translation. RNA in situ conformation sequencing (RIC-seq) is a technique for capturing protein-mediated RNA-RNA proximal… read more here.
Keywords: rna rna; rna; rna interactions; ric seq ... See more keywords
Zooming in on protein–RNA interactions: a multi-level workflow to identify interaction partners
Sign Up to like & getrecommendations! Published in 2020 at "Biochemical Society Transactions"
DOI: 10.1042/bst20191059
Abstract: Interactions between proteins and RNA are at the base of numerous cellular regulatory and functional phenomena. The investigation of the biological relevance of non-coding RNAs has led to the identification of numerous novel RNA-binding proteins… read more here.
Keywords: identify; protein rna; zooming protein; rna ... See more keywords
Protein–RNA interactions: from mass spectrometry to drug discovery
Sign Up to like & getrecommendations! Published in 2023 at "Essays in Biochemistry"
DOI: 10.1042/ebc20220177
Abstract: Abstract Proteins and RNAs are fundamental parts of biological systems, and their interactions affect many essential cellular processes. Therefore, it is crucial to understand at a molecular and at a systems level how proteins and… read more here.
Keywords: drug discovery; mass spectrometry; spectroscopy; protein rna ... See more keywords
Experimental and computational methods for studying the dynamics of RNA-RNA interactions in SARS-COV2 genomes.
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in functional genomics"
DOI: 10.1093/bfgp/elac050
Abstract: Long-range ribonucleic acid (RNA)-RNA interactions (RRI) are prevalent in positive-strand RNA viruses, including Beta-coronaviruses, and these take part in regulatory roles, including the regulation of sub-genomic RNA production rates. Crosslinking of interacting RNAs and short… read more here.
Keywords: experimental computational; long range; rna; rna interactions ... See more keywords
An ensemble approach to predict binding hotspots in protein-RNA interactions based on SMOTE data balancing and Random Grouping feature selection strategies
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac138
Abstract: MOTIVATION The identification of binding hotspots in protein-RNA interactions is crucial for understanding their potential recognition mechanisms and drug design. The experimental methods have many limitations, since they are usually time-consuming and labor-intensive. Thus, developing… read more here.
Keywords: binding hotspots; random grouping; protein rna; hotspots protein ... See more keywords