Protein–RNA interactions: structural biology and computational modeling techniques

S Jones - Biophysical reviews, 2016 - Springer
RNA-binding proteins are functionally diverse within cells, being involved in RNA-
metabolism, translation, DNA damage repair, and gene regulation at both the transcriptional …

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 …

Molecular modeling applied to nucleic acid-based molecule development

A Krüger, FM Zimbres, T Kronenberger, C Wrenger - Biomolecules, 2018 - mdpi.com
Molecular modeling by means of docking and molecular dynamics (MD) has become an
integral part of early drug discovery projects, enabling the screening and enrichment of large …

On the use of knowledge-based potentials for the evaluation of models of protein–protein, protein–DNA, and protein–RNA interactions

O Fornes, J Garcia-Garcia, J Bonet, B Oliva - Advances in protein chemistry …, 2014 - Elsevier
Proteins are the bricks and mortar of cells, playing structural and functional roles. In order to
perform their function, they interact with each other as well as with other biomolecules such …

P3DOCK: a protein–RNA docking webserver based on template-based and template-free docking

J Zheng, X Hong, J Xie, X Tong, S Liu - Bioinformatics, 2020 - academic.oup.com
Motivation The main function of protein–RNA interaction is to regulate the expression of
genes. Therefore, studying protein–RNA interactions is of great significance. The information …

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 …

Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation

S Rinaldi, E Moroni, R Rozza… - Journal of Chemical …, 2024 - ACS Publications
Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute
98–99% of the human genome. Non-coding RNAs encompass diverse functional classes …

Protein-RNA complexes and efficient automatic docking: expanding RosettaDock possibilities

A Guilhot-Gaudeffroy, C Froidevaux, J Azé, J Bernauer - PloS one, 2014 - journals.plos.org
Protein-RNA complexes provide a wide range of essential functions in the cell. Their atomic
experimental structure solving, despite essential to the understanding of these functions, is …

Thermodynamic database supports deciphering protein–nucleic acid interactions

LC Mei, GF Hao, GF Yang - Trends in Biotechnology, 2023 - cell.com
The thermodynamics of protein–nucleic acid interactions (PNIs) is crucial for elucidating the
mechanisms of molecular recognition and pathological consequences. The Protein–Nucleic …

[引用][C] Computational tools for investigating RNA-protein interaction partners

U Muppirala, D Dobbs, B Lewis - 2013