The DSSR paper has been published in Nucleic Acids Research

[xiangjun]

After numerous efforts, it is a real pleasure to see the publication of the paper titled "DSSR: an integrated software tool for dissecting the spatial structure of RNA" in Nucleic Acids Research.

Here is the abstract:

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/.

While only time can tell the impact of a scientific contribution, I feel confident to predict that, in the long run, the DSSR paper will receive many more citations than the 3DNA papers combined. With a unique balance of the description of novel methods and the illustrated new findings enabled by the software, the DSSR paper stands clearly at the very top among all my publications. I am also completely satisfied with the editing outcome in the final page-proof stage (going through three iterations, on issues of deleting a comma, changing dash–to-hyphen etc) before it is finalized for publication.

For those who are interested in details, I have added a new section titled "DSSR-NAR paper" with scripts and related data files for the reproduction of our reported results. As always, I welcome any comments, and I strive to respond promptly to each and every question you may have on the DSSR paper.

Xiang-Jun