The program automatically identifies and annotates base pairs ( 14, 15), detects higher-order coplanar base associations (triplet, quadruplet, etc.), finds coaxially stacked helices, characterizes loops of various types (hairpin, bulge, internal, and junction), and categorizes pseudoknots of arbitrary complexity, among numerous other functionalities ( 9). DSSR has a comprehensive and unique set of functionalities for the analysis of RNA 3D structures ( 12, 13). It has been designed to streamline the analysis and annotation of RNA tertiary structures using only an mmCIF or PDB file as input. DSSR is a component of the 3DNA suite of programs ( 10, 11) for the analysis, rebuilding, and visualization of 3D nucleic acid structures. The single-file DSSR binary executable is tiny (∼1MB) and self-contained (with zero dependencies), with an efficient and robust performance. The work presented here fills a gap in RNA structural bioinformatics, serving a huge user base both in research and education.ĭSSR, Dissecting the Spatial Structure of RNA, is a stand-alone, command-line program written in ANSI C ( 9). None of these tools, however, has the capability of selecting common RNA structural features and highlighting them in a 3D context interactively. Moreover, RNApdbee ( 8) extracts RNA secondary structure from 3D coordinates, and presents it in planar diagrams. Assemble ( 7) combines RNA secondary structure design with 3D modeling. VARNA ( 6) allows for interactive drawing and editing of RNA secondary structures. Jalview ( 5) is a program for editing, visualizing, and analyzing multiple sequence alignments. In addition to general-purpose 3D molecular viewers, quite a few tools are dedicated to RNA structures. However, the field of RNA structural bioinformatics is still lagging behind for example, most current molecular graphics tools lack built-in support even for base pairs, double helices or hairpin loops. α-helices and β-strands) are readily accessible via the de facto standard DSSP algorithm ( 1) and routinely featured in general-purpose molecular graphics programs, such as Jmol/JSmol ( 2, 3), the PyMOL molecular graphics system (version 1.8, Schrödinger, LLC), and the NGL viewer ( 4). For proteins, secondary structural components (e.g. Sophisticated analysis and visualizations are essential for making sense of the intricate 3D structures of macromolecules, providing insights into their diverse functions in essential biological processes. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website ). This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. However, the field of RNA structural bioinformatics is still lagging behind for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules.
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