[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"detail-sidebar-cat-0-en-105":3,"doc-seo-657881-105":59,"doc-detail-657881-en":130},{"code":4,"msg":5,"data":6},0,"success",[7,13,18,23,28,33,38,43,48,51,55],{"id":8,"doc_module":4,"doc_module_name":9,"category_name":10,"show_sort_weight":11,"slug":12},1,"Document","Story & Novel",90,"story-novel",{"id":14,"doc_module":4,"doc_module_name":9,"category_name":15,"show_sort_weight":16,"slug":17},2,"Literature",80,"literature",{"id":19,"doc_module":4,"doc_module_name":9,"category_name":20,"show_sort_weight":21,"slug":22},4,"Exam",70,"exam",{"id":24,"doc_module":4,"doc_module_name":9,"category_name":25,"show_sort_weight":26,"slug":27},5,"Comic",60,"comic",{"id":29,"doc_module":4,"doc_module_name":9,"category_name":30,"show_sort_weight":31,"slug":32},6,"Technology",50,"technology",{"id":34,"doc_module":4,"doc_module_name":9,"category_name":35,"show_sort_weight":36,"slug":37},7,"Healthcare",40,"healthcare",{"id":39,"doc_module":4,"doc_module_name":9,"category_name":40,"show_sort_weight":41,"slug":42},8,"Research & Report",30,"research-report",{"id":44,"doc_module":4,"doc_module_name":9,"category_name":45,"show_sort_weight":46,"slug":47},9,"Religion & Spirituality",20,"religion-spirituality",{"id":46,"doc_module":4,"doc_module_name":9,"category_name":49,"show_sort_weight":46,"slug":50},"World Cup","world-cup",{"id":52,"doc_module":4,"doc_module_name":9,"category_name":53,"show_sort_weight":52,"slug":54},10,"Lifestyle","lifestyle",{"id":56,"doc_module":4,"doc_module_name":9,"category_name":57,"show_sort_weight":24,"slug":58},19,"General","general",{"code":4,"msg":60,"data":61},"ok",{"site_id":62,"language":63,"slug":64,"title":65,"keywords":66,"description":67,"schema_data":68,"social_meta":123,"head_meta":125,"extra_data":127,"updated_unix":129},105,"en","ribodraw-semiautomated-two-dimensional-drawing-of-rna-tertiary-structure-diagrams","RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams","","RNA three-dimensional (3D) structure publication, discussion, and modeling depend on accurate two-dimensional (2D) drawings that highlight functional features such as noncanonical base pairs and protein contacts. RiboDraw introduces semiautomated software dedicated to generating these 2D RNA tertiary-structure diagrams. The method is demonstrated across multiple RNAs, including E. coli tRNA-Phe, Tetrahymena ribozyme P4–P6, a viral −1 frameshift element, and SARS-CoV-2 5’ UTR.",{"@graph":69,"@context":122},[70,84,105],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/ribodraw-semiautomated-two-dimensional-drawing-of-rna-tertiary-structure-diagrams/657881/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/ribodraw-semiautomated-two-dimensional-drawing-of-rna-tertiary-structure-diagrams/657881.png","ImageObject",300,407,{"name":92,"@type":93},"Angel","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-29","2026-10-26",true,{"@type":102,"interactionType":103,"userInteractionCount":29},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"What problem does RiboDraw address in RNA structural visualization?","Question",{"text":112,"@type":113},"It addresses the labor needed to manually refine 2D RNA drawings so they convey key tertiary fold relationships, which conventional tooling often omits.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"Which kinds of RNA features are emphasized in RiboDraw-generated diagrams?",{"text":117,"@type":113},"Diagrams depict functional elements including noncanonical base pairs and protein contacts, and they reflect relative positions in 3D space.",{"name":119,"@type":110,"acceptedAnswer":120},"How can RiboDraw be obtained and used?",{"text":121,"@type":113},"RiboDraw is provided as a MATLAB package available freely via the referenced GitHub repository.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},657881,1793096594,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":29,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":52,"language":139,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":140,"faqs":141,"seo_title":142,"seo_description":67,"update_tm":143,"read_time":144},687207412472,"https://ap-avatar.wpscdn.com/davatar_155a257f0dc6eb9ab79c44ca47cae57d","Published online 14 October 2021 NAR Genomics and Bioinformatics, 2021, Vol. 3, No. 4 1  \n[https://doi.org/10.1093/nargab/lqab091](https://doi.org/10.1093/nargab/lqab091)  \nRiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams  \nRhiju Das 1,2,* and Andrew M. Watkins 2  \n1 Department of Physics, Stanford University, Stanford, CA 94305, USA and 2 Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA  \nReceived June 01, 2021; Revised September 06, 2021; Editorial Decision September 07, 2021; Accepted October 08, 2021  \nABSTRACT  \nPublishing, discussing, envisioning, modeling, designing and experimentally determining RNA threedimensional (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, includingthe 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](https://github.com/DasLab/RiboDraw).  \nINTRODUCTION  \nTwo-dimensional (2D) depictions of RNA secondary structure serve two purposes. For the authors making them, the analysis ensures thoughtful inspection of a threedimensional (3D) molecule and distillation of its most important functional features into a human-understandable form. For readers, 2D drawings provide an entry point into complex structures, allowing for a gradual familiarization with increasing levels of detail. Over decades of publishing and presentation, a conventional ‘visual language’ for depicting RNA tertiary structure in 2D drawings has emerged, but the tooling available remains laborious.  \nYears of researchers communicating about RNA structure have established common standards to facilitate common understanding. Helices are typically drawn in horizontal or vertical orientations; sets of shapes convey the details of base pairing geometry (Leontis–Westhof annotations)  \n(1); numbers are provided every 10th nucleotide; and helices, or stacked sets of stems, are given names for easy reference (Figure 1) . Most importantly, something about 2D layouts should convey tertiary fold, with regions in close contact in 3D also in close contact in 2D––and this remains difficult to guarantee unless the layouts are hand drawn. Asan illustration, Figure 1 shows previously available drawings of the 16S rRNA of the Escherichia coli ribosome small subunit. We indicate with arrows the depiction of h33 in each drawing, which bends back in the 3􀀂 major domain to form a tertiary contact with h32; the resulting shape forms a beaklike 3D structure in the molecule’s ‘head’. None of the 2D layouts in Figure 1A–C conveys that shape. Although there are multiple packages in wide use that implement several of the conventions for drawing 2D layouts, such as XRNA (2) and VARNA (3), no previous software directly implements each one, with the conveyance of tertiary arrangements being an almost universal omission. Consequently, a secondary structure depiction that reflects each of these principles to date, such as that in Figure 1D(4), has required tedious manual refinement in general packages like Adobe Illustrator or Microsoft PowerPoint.  \nThis shortcoming has been amplified by the increasing throughput of structure determination efforts and, at the same time, the scale of the structures under study. In particular, the development of s","cbCaiiQK6B3joRWH","https://ap.wps.com/l/cbCaiiQK6B3joRWH","pdf",9176912,"English","# Abstract\n# Introduction","[{\"question\":\"What problem does RiboDraw address in RNA structural visualization?\",\"answer\":\"It addresses the labor needed to manually refine 2D RNA drawings so they convey key tertiary fold relationships, which conventional tooling often omits.\"},{\"question\":\"Which kinds of RNA features are emphasized in RiboDraw-generated diagrams?\",\"answer\":\"Diagrams depict functional elements including noncanonical base pairs and protein contacts, and they reflect relative positions in 3D space.\"},{\"question\":\"How can RiboDraw be obtained and used?\",\"answer\":\"RiboDraw is provided as a MATLAB package available freely via the referenced GitHub repository.\"}]","RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams | PDF",1792993336,25]