RNA‐protein interactions in an unstructured context
B Zagrovic, L Bartonek, AA Polyansky - FEBS letters, 2018 - Wiley Online Library
Despite their importance, our understanding of noncovalent RNA–protein interactions is
incomplete. This especially concerns the binding between RNA and unstructured protein …
incomplete. This especially concerns the binding between RNA and unstructured protein …
Protein–RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures
Motivation: The recognition of specific RNA sequences and structures by proteins is critical
to our understanding of RNA processing, gene expression and viral replication. The diversity …
to our understanding of RNA processing, gene expression and viral replication. The diversity …
The role of RNA sequence and structure in RNA–protein interactions
A Gupta, M Gribskov - Journal of molecular biology, 2011 - Elsevier
We investigate the sequence and structural properties of RNA–protein interaction sites in
211 RNA–protein chain pairs, the largest set of RNA–protein complexes analyzed to date …
211 RNA–protein chain pairs, the largest set of RNA–protein complexes analyzed to date …
Prediction of interacting single-stranded RNA bases by protein-binding patterns
Prediction of protein–RNA interactions at the atomic level of detail is crucial for our ability to
understand and interfere with processes such as gene expression and regulation. Here, we …
understand and interfere with processes such as gene expression and regulation. Here, we …
Predicting novel RNA–RNA interactions
IM Meyer - Current opinion in structural biology, 2008 - Elsevier
The purpose of this article is to give a brief, yet concise overview of the current
computational methods for predicting novel RNA–RNA interactions, that is interactions …
computational methods for predicting novel RNA–RNA interactions, that is interactions …
A knowledge‐based potential function predicts the specificity and relative binding energy of RNA‐binding proteins
S Zheng, TA Robertson, G Varani - The FEBS journal, 2007 - Wiley Online Library
RNA–protein interactions are fundamental to gene expression. Thus, the molecular basis for
the sequence dependence of protein–RNA recognition has been extensively studied …
the sequence dependence of protein–RNA recognition has been extensively studied …
Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA–protein complexes
A set of> 300 nonredundant high-resolution RNA–protein complexes were rigorously
searched for π-contacts between an amino acid side chain (W, H, F, Y, R, E and D) and an …
searched for π-contacts between an amino acid side chain (W, H, F, Y, R, E and D) and an …
Dissecting the protein–RNA interface: the role of protein surface shapes and RNA secondary structures in protein–RNA recognition
Protein–RNA interactions are essential for many biological processes. However, the
structural mechanisms underlying these interactions are not fully understood. Here, we …
structural mechanisms underlying these interactions are not fully understood. Here, we …
Computational biology of RNA interactions
C Dieterich, PF Stadler - Wiley Interdisciplinary Reviews: RNA, 2013 - Wiley Online Library
The biodiversity of the RNA world has been underestimated for decades. RNA molecules
are key building blocks, sensors, and regulators of modern cells. The biological function of …
are key building blocks, sensors, and regulators of modern cells. The biological function of …
Conformational readout of RNA by small ligands
E Kligun, Y Mandel-Gutfreund - RNA biology, 2013 - Taylor & Francis
RNA molecules have highly versatile structures that can fold into myriad conformations,
providing many potential pockets for binding small molecules. The increasing number of …
providing many potential pockets for binding small molecules. The increasing number of …