Computational methods for prediction of protein–RNA interactions

T Puton, L Kozlowski, I Tuszynska, K Rother… - Journal of structural …, 2012 - Elsevier
Understanding the molecular mechanism of protein–RNA recognition and complex
formation is a major challenge in structural biology. Unfortunately, the experimental …

[HTML][HTML] Template-based modeling of protein-RNA interactions

J Zheng, PJ Kundrotas, IA Vakser… - PLoS computational …, 2016 - journals.plos.org
Protein-RNA complexes formed by specific recognition between RNA and RNA-binding
proteins play an important role in biological processes. More than a thousand of such …

Computational modeling of protein–RNA complex structures

I Tuszynska, D Matelska, M Magnus, G Chojnowski… - Methods, 2014 - Elsevier
Protein–RNA interactions play fundamental roles in many biological processes, such as
regulation of gene expression, RNA splicing, and protein synthesis. The understanding of …

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 …

Predictions of protein–RNA interactions

D Cirillo, F Agostini, GG Tartaglia - Wiley Interdisciplinary …, 2013 - Wiley Online Library
Ribonucleoprotein interactions play important roles in a wide variety of cellular processes,
ranging from transcriptional and posttranscriptional regulation of gene expression to host …

Quantifying sequence and structural features of protein–RNA interactions

S Li, K Yamashita, KM Amada… - Nucleic acids …, 2014 - academic.oup.com
Increasing awareness of the importance of protein–RNA interactions has motivated many
approaches to predict residue-level RNA binding sites in proteins based on sequence or …

[HTML][HTML] Computational prediction of RNA-binding proteins and binding sites

J Si, J Cui, J Cheng, R Wu - International journal of molecular sciences, 2015 - mdpi.com
Proteins and RNA interaction have vital roles in many cellular processes such as protein
synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and …

RNABindR: a server for analyzing and predicting RNA-binding sites in proteins

M Terribilini, JD Sander, JH Lee, P Zaback… - Nucleic acids …, 2007 - academic.oup.com
Understanding interactions between proteins and RNA is key to deciphering the
mechanisms of many important biological processes. Here we describe RNABindR, a web …

Prediction of RNA binding proteins comes of age from low resolution to high resolution

H Zhao, Y Yang, Y Zhou - Molecular BioSystems, 2013 - pubs.rsc.org
Networks of protein–RNA interactions is likely to be larger than protein–protein and protein–
DNA interaction networks because RNA transcripts are encoded tens of times more than …

Protein–RNA interactions: structural characteristics and hotspot amino acids

DM Krüger, S Neubacher, TN Grossmann - Rna, 2018 - rnajournal.cshlp.org
Structural information about protein–RNA complexes supports the understanding of crucial
recognition processes in the cell, and it can allow the development of high affinity ligands to …