DSSR has been published, and its results are reproducible

It is a great pleasure to note that a paper titled DSSR, an integrated software tool for dissecting the spatial structure of RNA has recently been published in Nucleic Acids Research (NAR). Co-authored by Harmen Bussemaker, Wilma Olson and me (a team with a unique combination of complementary expertise), this DSSR paper represents another solid piece of work that I feel proud of. In contrast to our previous GpU dinucleotide platform paper focusing on results, and the two major 3DNA papers concentrating on methods, the current NAR article describes significant scientific findings that are enabled by the novel analysis algorithms implemented in the program. Moreover, DSSR introduces an appealing and highly informative “cartoon-block” representation of RNA structures that combines PyMOL cartoon schematics with 3DNA base color-coded rectangular blocks.

The abstract of the paper is quoted below:

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://home.x3dna.org/.

During the review process, we are delighted that the referees confirmed the claim that we made in the cover letter: “We would also like to emphasize that our reported results are easily verifiable, and we assure rigorous reproducibility of the data and figures described in this article.” Now that the paper has been published, as a follow-up, I’ve made available all the scripts and data files associated with the paper in a new section DSSR-NAR paper on the 3DNA Forum. The DSSR User Manual has also been updated with additional, previously undocumented, auxiliary options.

Overall, it took me more than ten days to create the 19 posts in the DSSR-NAR paper section and to revise the DSSR User Manual, along with other minor refinements for consistency. During the process, I’ve tried to make the scripts and data files self-contained for wide accessibility and easy understanding.

Any interested party should now be able to reproduce the table and figures (including the supplementary data) reported in the article. Moreover, with the additional details given in the post RNA cartoon-block representations with PyMOL and DSSR, one can easily generate similar schematic images as shown below:

yeast phenylalanine tRNA (1ehz) with base blocks yeast phenylalanine tRNA (1ehz) with WC base-pair blocks
1msy: with the minor groove edge (black) of the C-G pair that closes the GUAA tetraloop facing the viewer 27-nt rRNA fragment with GUAA tetraloop (1msy) -- base blocks in outline

I feel confident to claim that the results reported in our DSSR paper are reproducible. If you have issues related to the paper, please post them on the 3DNA Forum. I strive to respond promptly to any questions asked there.

In summary, DSSR is an integrated computational tool, designed from the bottom up to streamline the analysis of RNA three-dimensional structures. It is built upon my extensive experience in supporting 3DNA, growing knowledge of RNA structures, and refined programming skills. DSSR has a combined set of functionalities well beyond the scope of any known specialized resources. The program may well serve as a cornerstone for RNA structural bioinformatics and will benefit a broad range of possible applications.





Thank you for printing this article from http://home.x3dna.org/. Please do not forget to visit back for more 3DNA-related information. — Xiang-Jun Lu