How RNA-binding proteins interact with RNA: molecules and mechanisms

M Corley, MC Burns, GW Yeo - Molecular cell, 2020 - cell.com
RNA-binding proteins (RBPs) comprise a large class of over 2,000 proteins that interact with
transcripts in all manner of RNA-driven processes. The structures and mechanisms that …

Comprehensive review and empirical analysis of hallmarks of DNA-, RNA-and protein-binding residues in protein chains

J Zhang, Z Ma, L Kurgan - Briefings in bioinformatics, 2019 - academic.oup.com
Proteins interact with a variety of molecules including proteins and nucleic acids. We review
a comprehensive collection of over 50 studies that analyze and/or predict these interactions …

Intrinsic disorder in human RNA-binding proteins

B Zhao, A Katuwawala, CJ Oldfield, G Hu, Z Wu… - Journal of Molecular …, 2021 - Elsevier
Although RNA-binding proteins (RBPs) are known to be enriched in intrinsic disorder, no
previous analysis focused on RBPs interacting with specific RNA types. We fill this gap with …

Bioinformatics tools and benchmarks for computational docking and 3D structure prediction of RNA-protein complexes

C Nithin, P Ghosh, JM Bujnicki - Genes, 2018 - mdpi.com
RNA-protein (RNP) interactions play essential roles in many biological processes, such as
regulation of co-transcriptional and post-transcriptional gene expression, RNA splicing …

Label‐Free Electrophoretic Mobility Shift Assay (EMSA) for Measuring Dissociation Constants of Protein‐RNA Complexes

M Seo, L Lei, M Egli - Current protocols in nucleic acid …, 2019 - Wiley Online Library
The electrophoretic mobility shift assay (EMSA) is a well‐established method to detect
formation of complexes between proteins and nucleic acids and to determine, among other …

An account of solvent accessibility in protein-RNA recognition

S Mukherjee, RP Bahadur - Scientific reports, 2018 - nature.com
Protein–RNA recognition often induces conformational changes in binding partners.
Consequently, the solvent accessible surface area (SASA) buried in contact estimated from …

Molecular architecture of protein-RNA recognition sites

A Barik, SP Pilla, RP Bahadur - Journal of Biomolecular Structure …, 2015 - Taylor & Francis
The molecular architecture of protein-RNA interfaces are analyzed using a non-redundant
dataset of 152 protein-RNA complexes. We find that an average protein-RNA interface is …

A non‐redundant protein–RNA docking benchmark version 2.0

C Nithin, S Mukherjee… - … : Structure, Function, and …, 2017 - Wiley Online Library
We present an updated version of the protein–RNA docking benchmark, which we first
published four years back. The non‐redundant protein–RNA docking benchmark version 2.0 …

Computational resources for understanding the effect of mutations in binding affinities of protein–RNA complexes

K Harini, SR Krishnan, M Sekijima… - … on Structure, Functions …, 2025 - World Scientific
Protein–nucleic acid interactions play a crucial role in maintaining cellular homeostasis.
Quantitatively, these interactions are described in terms of the dissociation constant or free …

EPDRNA: a model for identifying DNA–RNA binding sites in disease-related proteins

CZ Sun, YE Feng - The Protein Journal, 2024 - Springer
Protein–DNA and protein–RNA interactions are involved in many biological processes and
regulate many cellular functions. Moreover, they are related to many human diseases. To …