Recently I noticed two new citations to DSSR, an integrated software tool for dissecting the spatial structure of RNA. One is from the Yesselman et al. article Computational design of three-dimensional RNA structure and function in Nature Nanotechnology, and the other is from the Wang et al. article 3dRNA v2.0: An Updated Web Server for RNA 3D Structure Prediction in International Journal of Molecular Sciences.
Yesselman et al. has used DSSR in RNAMake for building the motif library. The relevant section is as follows:
We processed each RNA structure to extract every motif with Dissecting the Spatial Structure of RNA (DSSR)54 with the following command:
x3dna-dssr –i file.pdb –o file_dssr.out
We manually checked each extracted motif to confirm that it was the correct type, as DSSR sometimes classifies tertiary contacts as higher-order junctions and vice versa. For each motif collected from DSSR, we ran the X3DNA find_pair and analyze programs to determine the reference frame for the first and last base pair of each motif to allow for the alignment between motifs:
find_pair file.pdb 2> /dev/null stdout | analyze stdin >& /dev/null
It is worth noting the sentence that “DSSR sometimes classifies tertiary contacts as higher-order junctions and vice versa.” Presumably. the authors are referring to the inclusion of ‘isolated canonical pairs’ in junctions by default in DSSR. Overall, the default DSSR settings follow the most common practice in RNA literature. In the meantime, I am aware that the community may not agree on every detail. Thus DSSR provide many options (documented or otherwise) to cater for other potential use cases. See the Stems of junction structure have only one base pair and Junction definition threads on the 3DNA Forum for two examples. In the long run, DSSR is likely to help consolidate RNA nomenclature that can be applied in a pragmatic, consistent manner.
Note also that DSSR provides the reference frame of each identified base pair via the JSON option. Using
1ehz as an example, the following command provides detailed information about base pairs:
x3dna-dssr -i=1ehz.pdb --json --more | jq .pairs
In the 3dRNA 2.0 paper, DSSR is cited as below. This is the first time DSSR is integrated in the 3dRNA pipeline.
The predicted structures are built from the sequence and secondary structure, while the former is obtained from their native structures fetched from PDB (https://www.rcsb.org/), and the latter is calculated from DSSR (Dissecting the Spatial Structure of RNA) .