A paper titled "DSSR, an integrated software tool for dissecting the spatial structure of RNA" recently appeared in *Nucleic Acids Research* ( http://nar.oxfordjournals.org/cgi/content/full/gkv716). Starting from a three-dimensional atomic coordinate file in either PDB or PDBx/mmCIF format, DSSR, the new software product described in the paper, analyzes and annotates RNA tertiary structures and uncovers a broad range of structural features in a consistent and easily accessible framework. The software is implemented in ANSI C as a stand-alone, command-line program and is self-contained. The binaries for common operating systems (Mac OS X, Linux, and Windows) are tiny (<1MB), without runtime dependencies on third-party libraries. DSSR is efficient and robust due to comprehensive tests against all nucleic-acid-containing structures in the PDB and continued refinements based on user feedback.
DSSR identifies canonical and noncanonical base pairs, including those with modified nucleotides, in any tautomeric or protonation state. The software detects higher-order (three or more) coplanar base associations, termed multiplets. It finds arrays of stacked pairs, classifies them by base-pair identity and backbone connectivity, and distinguishes a stem of covalently connected canonical pairs from a helix of stacked pairs of arbitrary type/linkage. DSSR also pinpoints the coaxial stacking of multiple stems within a single helix and lists the isolated canonical pairs that lie outside of a stem. The program characterizes "closed" loops of various types (hairpin, bulge, internal, and junction loops) and pseudoknots of high complexity. Notably, DSSR employs isolated pairs and the ends of stems, whether pseudoknotted or not, to define junction loops. This new, inclusive definition provides a novel perspective on the spatial organization of RNA, even for small molecules such as the viral tRNA mimic from turnip yellow mosaic virus and the *env22* twister ribozyme. In short, DSSR is to RNA what DSSP is to proteins for defining secondary structures, but with more functionality: DSSR includes quantitative descriptions of local base-pair geometry; assignments of common names and classifications of base pairs; listings of commonly used sugar-phosphate backbone parameters, continuous base stacks, and non-pairing interactions (including those involving phosphate groups); and detections of ribose zipper motifs, A-minor motifs, G-tetrads, U-turns, kissing loops, and kink-turns. The publication includes significant new scientific findings that are enabled by the innovative analysis algorithms implemented in the software. Moreover, the paper introduces an appealing and highly informative "cartoon-block" representation of RNA structure that combines PyMOL cartoon schematics with color-coded rectangular base (or base-pair) blocks. As a follow-up to the publication, the 3DNA Forum includes all of the scripts and data files associated with the article in a new section titled "DSSR-NAR paper" (http://forum.x3dna.org/dssr-nar-paper/). The Forum also contains links to an updated version of the DSSR User Manual ( http://x3dna.bio.columbia.edu/docs/dssr-manual.pdf). Any interested party should be able to reproduce the tabulated data and figures (including the supplementary data) reported in the article. Moreover, with the details provided in "RNA cartoon-block representations with PyMOL and DSSR" ( http://forum.x3dna.org/dssr-nar-paper/rna-cartoon-block-representations-with-pymol-and-dssr/), schematic images identical to those in the paper and the post can be easily generated. Any questions related to the paper are welcomed on the 3DNA Forum. Dr. Xiang-Jun Lu, the lead author of the paper and the person spearheading the Forum, aims to respond promptly to any reported issues. [This message is cross-posted on ccp4bb, pdb-l, and pymol-users. I apologize for any duplicate copies you may receive.] Xiang-Jun -- Xiang-Jun Lu (PhD) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/
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