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 …

[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 …

NPDock: a web server for protein–nucleic acid docking

I Tuszynska, M Magnus, K Jonak… - Nucleic acids …, 2015 - academic.oup.com
Protein–RNA and protein–DNA interactions play fundamental roles in many biological
processes. A detailed understanding of these interactions requires knowledge about protein …

A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method

SY Huang, X Zou - Nucleic acids research, 2014 - academic.oup.com
Protein-RNA interactions play important roles in many biological processes. Given the high
cost and technique difficulties in experimental methods, computationally predicting the …

Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein–RNA complexes

F Chen, H Sun, J Wang, F Zhu, H Liu, Z Wang, T Lei… - Rna, 2018 - rnajournal.cshlp.org
Molecular docking provides a computationally efficient way to predict the atomic structural
details of protein–RNA interactions (PRI), but accurate prediction of the three-dimensional …

[HTML][HTML] Evaluating native-like structures of RNA-protein complexes through the deep learning method

C Zeng, Y Jian, S Vosoughi, C Zeng, Y Zhao - Nature Communications, 2023 - nature.com
RNA-protein complexes underlie numerous cellular processes, including basic translation
and gene regulation. The high-resolution structure determination of the RNA-protein …

[HTML][HTML] Hypoxia-induced exosomal circPDK1 promotes pancreatic cancer glycolysis via c-myc activation by modulating miR-628-3p/BPTF axis and degrading BIN1

J Lin, X Wang, S Zhai, M Shi, C Peng, X Deng… - Journal of Hematology & …, 2022 - Springer
Background circRNA has been established to play a pivotal role in tumorigenesis
development in a variety of cancers; nevertheless, the biological functions and molecular …

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 …

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 …

LigandRNA: computational predictor of RNA–ligand interactions

A Philips, K Milanowska, G Łach, JM Bujnicki - Rna, 2013 - rnajournal.cshlp.org
RNA molecules have recently become attractive as potential drug targets due to the
increased awareness of their importance in key biological processes. The increase of the …