As mentioned in the blog post Integrating DSSR into Jmol and PyMOL,
“The small size, zero configuration, extensive features, and robust performance make DSSR ideal to be integrated into other bioinformatics tools.” In addition to the DSSR-Jmol and DSSR-PyMOL integrations which I initiated and got personally involved, other bioinformatics resources are increasingly taking advantage of what DSSR has to offer. Here are a few examples:
- As of Nov. 7, 2017, DSSR has become the only option for base-pairing annotation in the WebSTAR3D web server for RNA 3D structure alignment. In the 2016 WebSTAR3D publication in Bioinformatics, DSSR was the second choice, as shown in the excerpt below:
Before aligning structures, STAR3D preprocesses PDB files with base-pairing annotation using either MC-Annotate (Gendron et al., 2001; Lemieux and Major, 2002) (for PDB inputs) or DSSR (Lu et al., 2015) (for PDB and mmCIF inputs) and pseudo-knot removal using RemovePseudoknots (Smit et al., 2008).
- In the RNApdbee 2.0 web server for RNA secondary structure annotation, DSSR is the default option for identifying base pairs. See also the corresponding publication in Nucleic Acids Research (2018), titled RNApdbee 2.0: multifunctional tool for RNA structure annotation. In contrast, the first version (published in 2014) of RNApdbee put DSSR as the third option, following RNAView and MC-Annotate. See my blog post titled RNA pseudoknot detection and removal with DSSR, and the excerpts from the 2014 (RNApdbee) and 2018 (RNApdbee 2.0) papers:
2014, RNApdbee: In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs.
2018, RNApdbee 2.0: Base pairs can be identified by 3DNA/DSSR (default) (4), RNAView (5), MC-Annotate (3) or newly added FR3D (15).
- The Universe of RNA Structures (URS) web-interface to the URS database (URSDB) makes extensive use of DSSR. For each analyzed structure (including PDB entries), the DSSR text output file (termed “DSSR-file”) is also available. Impressively, the maintainers of URS are quick with DSSR updates. The current version used by the URS website is DSSR v1.7.4-2018jan30.
Forty years after the yeast phenylalanine tRNA structure was solved, modified nucleotides should no longer be an issue for RNA structural analysis, especially for this classic molecule. Automatic processing of modified nucleotides is just one aspect of DSSR’s substantial set of features. Based on my understanding of the field, more structural bioinformatics resources/tools could benefit from DSSR. Simply put, if one’s project is related to 3D DNA or RNA structures, DSSR may be of certain help. It’s just a timing issue that DSSR would benefit a (much) larger community.
