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
The role of the protein–RNA recognition code in neurodegeneration
Sign Up to like & getrecommendations! Published in 2019 at "Cellular and Molecular Life Sciences"
DOI: 10.1007/s00018-019-03096-3
Abstract: MicroRNAs are small endogenous RNAs that pair and bind to sites on mRNAs to direct post-transcriptional repression. However, there is a possibility that microRNAs directly influence protein structure and activity, and this influence can be… read more here.
Keywords: protein; recognition code; code; proteins involved ... See more keywords
Protein-RNA complexation driven by the charge regulation mechanism.
Sign Up to like & getrecommendations! Published in 2018 at "Biochemical and biophysical research communications"
DOI: 10.1016/j.bbrc.2017.07.027
Abstract: Electrostatic interactions play a pivotal role in many (bio)molecular association processes. The molecular organization and function in biological systems are largely determined by these interactions from pure Coulombic contributions to more peculiar mesoscopic forces due… read more here.
Keywords: regulation mechanism; mechanism; complexation; charge regulation ... See more keywords
Integrated structural biology to unravel molecular mechanisms of protein-RNA recognition.
Sign Up to like & getrecommendations! Published in 2017 at "Methods"
DOI: 10.1016/j.ymeth.2017.03.015
Abstract: Recent advances in RNA sequencing technologies have greatly expanded our knowledge of the RNA landscape in cells, often with spatiotemporal resolution. These techniques identified many new (often non-coding) RNA molecules. Large-scale studies have also discovered… read more here.
Keywords: unravel molecular; protein rna; biology; rna recognition ... See more keywords
QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods.
Sign Up to like & getrecommendations! Published in 2018 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.8b00670
Abstract: Although atomistic explicit-solvent Molecular Dynamics (MD) is a popular tool to study protein-RNA recognition, satisfactory MD description of protein-RNA complexes is not always achieved. Unfortunately, it is often difficult to separate MD simulation instabilities primarily… read more here.
Keywords: rna; calculations protein; rna complexes; protein rna ... See more keywords
Trisubstituted Pyrrolinones as Small-Molecule Inhibitors Disrupting the Protein–RNA Interaction of LIN28 and Let-7
Sign Up to like & getrecommendations! Published in 2021 at "ACS Medicinal Chemistry Letters"
DOI: 10.1021/acsmedchemlett.0c00546
Abstract: Modulation of protein–RNA interaction (PRI) using small molecules is a promising strategy to develop therapeutics. LIN28 is an RNA-binding protein that blocks the maturation of the tumor suppressor let-7 microRNAs. Herein, we performed a fluorescence… read more here.
Keywords: protein; rna interaction; lin28; interaction ... See more keywords
Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes
Sign Up to like & getrecommendations! Published in 2020 at "Nature Communications"
DOI: 10.1038/s41467-020-18543-0
Abstract: While the field of microbiology has adapted to the study of complex microbiomes via modern meta-omics techniques, we have not updated our basic knowledge regarding the quantitative levels of DNA, RNA and protein molecules within… read more here.
Keywords: integration absolute; within mixed; rna; protein rna ... See more keywords
PRIME-3D2D is a 3D2D model to predict binding sites of protein–RNA interaction
Sign Up to like & getrecommendations! Published in 2020 at "Communications Biology"
DOI: 10.1038/s42003-020-1114-y
Abstract: Protein-RNA interaction participates in many biological processes. So, studying protein–RNA interaction can help us to understand the function of protein and RNA. Although the protein–RNA 3D3D model, like PRIME, was useful in building 3D structural complexes,… read more here.
Keywords: rna interaction; prime 3d2d; predict binding; binding sites ... 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
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