Das Rhiju, Watkins Andrew M
Department of Physics, Stanford University, Stanford, CA 94305, USA.
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
NAR Genom Bioinform. 2021 Oct 14;3(4):lqab091. doi: 10.1093/nargab/lqab091. eCollection 2021 Dec.
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 tRNA-Phe, the P4-P6 domain of 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 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.
发表、讨论、设想、建模、设计并通过实验确定RNA三维（3D）结构，都需要制备二维（2D）绘图，以描绘目标分子的关键功能特征，如非经典碱基对和与蛋白质的相互作用。在此，我们介绍了一款用于绘制这些图形的新软件RiboDraw。我们通过将RiboDraw应用于几种RNA来展示其功能，这些RNA包括苯丙氨酸tRNA、核酶的P4-P6结构域、来自甜菜西方黄化病毒的-1核糖体移码刺激元件以及严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的5'非翻译区。我们展示了核糖体23S和16S亚基的二级结构图，这些图反映了非经典碱基对、核糖体蛋白和结构基序，并传达了这些关键特征在三维空间中的相对位置。该软件是一个MATLAB软件包，可在https://github.com/DasLab/RiboDraw上免费获取。
