CSSR: assignment of secondary structure to coarse‐grained RNA tertiary structures. Issue 4 (11th March 2022)

• Record Type: Journal Article
• Authors: Zhang, Chengxin; Pyle, Anna Marie
• Is Part Of: Acta crystallographica. Volume 78:Issue 4(2022)
• Page Start: 466
• Page End: 471
• Publication Date: 2022-03-11
• Subjects: RNA -- secondary‐structure assignment -- coarse‐grained structure model -- CSSR algorithm; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; Molecular biology -- Periodicals; Molecular structure -- Periodicals; Biomolecules -- Structure -- Periodicals; Cytology -- Periodicals; Biomolecules -- Structure; Crystallography; Cytology; Molecular biology; Molecular structure; X-ray crystallography; Periodicals; 548
• DOI: 10.1107/S2059798322001292
• Languages: English
• ISSNs: 2059-7983

Abstract

Abstract : CSSR, an algorithm for assigning secondary structures to RNA 3D structures with missing atoms, has been developed. The base‐pair assignment accuracy is close to 90% for 3D structures in which only one atom per nucleotide can be empirically identified. Abstract : RNA secondary‐structure (rSS) assignment is one of the most routine forms of analysis of RNA 3D structures. However, traditional rSS assignment programs require full‐atomic structures of the individual RNA nucleotides. This prevents their application to the modeling of RNA structures in which base atoms are missing. To address this issue, Coarse‐grained Secondary Structure of RNA ( CSSR ), an algorithm for the assignment of rSS for structures in which nucleobase atomic positions are incomplete, has been developed. Using CSSR, an rSS assignment accuracy of ∼90% is achieved even for RNA structures in which only one backbone atom per nucleotide is known. Thus, CSSR will be useful for the analysis of experimentally determined and computationally predicted RNA 3D structures alike. The source code of CSSR is available at https://github.com/pylelab/CSSR .