Automated 3D RNA structure prediction using the RNAComposer method for riboswitches

Methods in Enzymology
Katarzyna J PurzyckaRyszard W Adamiak

Abstract

Understanding the numerous functions of RNAs depends critically on the knowledge of their three-dimensional (3D) structure. In contrast to the protein field, a much smaller number of RNA 3D structures have been assessed using X-ray crystallography, NMR spectroscopy, and cryomicroscopy. This has led to a great demand to obtain the RNA 3D structures using prediction methods. The 3D structure prediction, especially of large RNAs, still remains a significant challenge and there is still a great demand for high-resolution structure prediction methods. In this chapter, we describe RNAComposer, a method and server for the automated prediction of RNA 3D structures based on the knowledge of secondary structure. Its applications are supported by other automated servers: RNA FRABASE and RNApdbee, developed to search and analyze secondary and 3D structures. Another method, RNAlyzer, offers new way to analyze and visualize quality of RNA 3D models. Scope and limitations of RNAComposer in application for an automated prediction of riboswitches' 3D structure will be presented and discussed. Analysis of the cyclic di-GMP-II riboswitch from Clostridium acetobutylicum (PDB ID 3Q3Z) as an example allows for 3D structure prediction of related ribo...Continue Reading

Citations

Jun 13, 2015·Nucleic Acids Research·Piotr LukasiakJacek Blazewicz
Apr 5, 2017·Annual Review of Biophysics·Zhichao Miao, Eric Westhof
Nov 18, 2017·International Journal of Molecular Sciences·Sha GongWenbing Zhang
Dec 14, 2017·Bioinformatics·Maciej AntczakMarta Szachniuk
Mar 28, 2018·Proceedings of the National Academy of Sciences of the United States of America·Anna V SherwoodTina M Henkin
Jan 14, 2017·Nucleic Acids Research·Denise Martinez-ZapienAnne-Catherine Dock-Bregeon
Aug 31, 2019·RNA Biology·Julita GumnaKatarzyna Pachulska-Wieczorek
Jun 9, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Joanna Miskiewicz, Marta Szachniuk
Aug 26, 2021·Nucleic Acids Research·Mariusz PopendaMarta Szachniuk
Dec 21, 2017·The Journal of Physical Chemistry. B·Xiaojun Xu, Shi-Jie Chen
Nov 2, 2021·The Journal of Physical Chemistry. B·Boyang ZhuoJingyuan Li

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