DSSR

Insight into the three-dimensional architecture of RNA is essential for
understanding its cellular functions. However, even the classic transfer RNA
structure contains features that are overlooked by existing bioinformatics tools.
Here we present DSSR (Dissecting the Spatial Structure of RNA), an integrated and
automated tool for analyzing and annotating RNA tertiary structures. The software
identifies canonical and noncanonical base pairs, including those with modified
nucleotides, in any tautomeric or protonation state. DSSR detects higher-order
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 identifies coaxial stacking of
multiple stems within a single helix and lists 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 arbitrary
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. Tests on all
nucleic acid structures in the Protein Data Bank confirm the efficiency and
robustness of the software, and applications to representative RNA molecules
illustrate its unique features. DSSR and related materials are freely available
at http://x3dna.org/.

DSSR: an integrated software tool for dissecting the spatial structure of RNA.

DSSR (Dissecting the Spatial Structure of RNA) is a software package to analyze, annotate, model, and visualize three-dimensional RNA and DNA tertiary structures.

DSSR

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