Recently, I noticed via Google Scholar the first citation to the paper DSSR, an integrated software tool for dissecting the spatial structure of RNA, recently published in Nucleic Acids Research (NAR). The citation is from Srinivas Somarowthu, in a review article titled Progress and current challenges in modeling large RNAs in the Journal of Molecular Biology. The JMB review article is concise, and overall a nice reading.

Specifically, in the section “Model Evaluation and Refinement”, DSSR is listed along with RNAView and MC-Annotate for the characterization of the secondary from 3D atomic coordinates, as below:

After building a model, it is essential to evaluate the quality, find any errors and refine the accordingly. First, it is important to make sure that all the base-pairs and the overall secondary structure is maintained correctly in the model. Tools such as RNAview [82], MC-Annotate [83], and DSSR [84] can calculate the secondary structure from a given 3D structure and thereby allow identification of problematic base-pairs. Recently, Antczak et al [85], developed a web server, RNApdbee, which integrates RNAview, MC-Annotate and DSSR, and extracts not only secondary structures but also kissing-loops and pseudoknots from a target tertiary model. Problematic base pairs can be fixed or rebuilt using interactive tools such as S2S/ASSEMBLE [45].

I am glad to see the first citation to the 2015 DSSR paper per se shortly after its publication in NAR. Looking forward, I can only expect more DSSR citations in diverse fields related to RNA structures.