Via Google Scholar, I noticed the following two citations to the DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL paper recently published in Nucleic Acids Research (NAR):
- Miskiewicz, Joanna, Joanna Sarzynska, and Marta Szachniuk. How bioinformatics resources work with G4 RNAs.” Briefings in Bioinformatics (2020).
- Caruso, Icaro Putinhon, et al. Dynamics of the N-terminal domain of SARS-CoV-2 nucleocapsid protein drives dsRNA melting in a counterintuitive tweezer-like mechanism. bioRxiv (2020).
Here are the direct quotations on the DSSR-PyMOL paper from these two citations.
The Miskiewicz et al. paper, in Briefings in Bioinformatics (2020):
DSSR [38] processes the 3D structure of the RNA molecule and annotates its secondary structure. It is a part of the 3DNA suite [67] designed to work with the structures of nucleic acids. DSSR identifies, classifies and describes base pairs, multiplets and characteristic motifs of the secondary structure; helices, stems, hairpin loops, bulges, internal loops, junctions and others. It can also detect modules and tertiary structure patterns, including pseudoknots and kink-turns. The recent extension, DSSR-PyMOL [68], allows drawing cartoon-block schemes of the 3D structure and responds to the need for simplified visualization of quadruplexes.
DSSR-PyMOL generated block schemes of both quadruplexes (Figure 4A3 and B3).
Figure 4: Visualization of (A) 2RQJ and (B) 6GE1 structures generated by (1) ElTetrado, (2) RNApdbee and (3) DSSR-PyMOL.
The Caruso et al. paper in bioRxiv (2020):
Next, the structural model of the N-NTD:dsTRS (5’–UCUAAAC–3’) complex was generated from the lowest-energy structure of the N-NTD:dsNS complex, derived from the cluster with the lowest HADDOCK score, by mutating the dsRNA sequence using w3DNA (29). Therefore, both complexes have identical geometries, varying only the dsRNA sequences. Structural conformation of the constructed model for N-NTD:dsTRS complex was displayed using the web application http://skmatic.x3dna.org for easy creation of DSSR (Dissecting the Spatial Structure of RNA)-PyMOL schematics (32).
Figure 1: Structural model of the N-NTD:dsRNA complex and its validation from molecular dynamics simulations. (A) Structural model of the N-NTD:dsTRS complex determined by molecular docking calculations and mutation of dsNS nucleotide sequence. N-NTD is presented as purple cartoon and dsTRS is denoted as a ribbon model with base pairing as colored rectangles. The color of the rectangles corresponds to the nitrogenous base of the dsRNA sense strand, namely A: red, C: yellow, U: cyan, and G: green. The large protruding β2-β3 loop is referred to as the finger. (B) …
p(clean)=.
Figure 3: Analysis of the intramolecular (dsRNAs) and intermolecular (N-NTD:dsRNAs) hydrogen bonds. (A) … (B) … (C) Structural model of the N-NTD:dsTRS complex representative of the MD simulation for run 5. The protein is shown in purple cartoon and dsTRS is denoted as a ribbon model with nitrogenous bases and base-pairing as colored squares and rectangles, respectively. The color of the squares corresponds to the type of nitrogenous base, namely A: red, C: yellow, U: cyan, and G: green, while the rectangles refer to the nitrogenous base color of the dsRNA sense strand.
It is really a pleasure to see the DSSR-PyMOL paper being cited quickly after its publication. I am always curious to see how DSSR is cited in literature. Indeed, over the years following citations to DSSR has become an effective way for me to become informed of directly relevant references. Reading these citing articles motivates me to further improve DSSR.
