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 …

Protein–RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures

N Morozova, J Allers, J Myers, Y Shamoo - Bioinformatics, 2006 - academic.oup.com
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 …

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 …

Prediction of interacting single-stranded RNA bases by protein-binding patterns

A Shulman-Peleg, M Shatsky, R Nussinov… - Journal of molecular …, 2008 - Elsevier
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 …

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 …

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 …

Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA–protein complexes

KA Wilson, RW Kung, S D'souza… - Nucleic Acids …, 2021 - academic.oup.com
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 …

Dissecting the protein–RNA interface: the role of protein surface shapes and RNA secondary structures in protein–RNA recognition

J Iwakiri, H Tateishi, A Chakraborty, P Patil… - Nucleic acids …, 2012 - academic.oup.com
Protein–RNA interactions are essential for many biological processes. However, the
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 …

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 …