RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams.
NAR Genom Bioinform
; 3(4): lqab091, 2021 Dec.
Article
in English
| MEDLINE | ID: covidwho-1475822
ABSTRACT
Publishing, discussing, envisioning, modeling, designing and experimentally determining RNA three-dimensional (3D) structures involve preparation of two-dimensional (2D) drawings that depict critical functional features of the subject molecules, such as noncanonical base pairs and protein contacts. Here, we describe RiboDraw, new software for crafting these drawings. We illustrate the features of RiboDraw by applying it to several RNAs, including the Escherichia coli tRNA-Phe, the P4-P6 domain of Tetrahymena ribozyme, a -1 ribosomal frameshift stimulation element from beet western yellows virus and the 5' untranslated region of SARS-CoV-2. We show secondary structure diagrams of the 23S and 16S subunits of the E. coli ribosome that reflect noncanonical base pairs, ribosomal proteins and structural motifs, and that convey the relative positions of these critical features in 3D space. This software is a MATLAB package freely available at https//github.com/DasLab/RiboDraw.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Language:
English
Journal:
NAR Genom Bioinform
Year:
2021
Document Type:
Article
Affiliation country:
Nargab
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