Fig 1.
Workflow of the PseudoknotVisualizer.
The software offers two usage options: a PyMOL extension and a Command Line Interface (CLI). The left figure illustrates the PyMOL extension, where a tertiary structure loaded into PyMOL (in this case, 5TPY) is analyzed and visualized by entering pkv 5TPY in the command line. This command applies color to the pseudoknot layers, with red indicating pseudoknot layer 1 and blue indicating layer 2, while additional layers (if present) can be visualized using other colors. Note that the entire molecule was pre-colored white to highlight the red and blue pseudoknot layers. The right figure demonstrates the CLI workflow. Like the PyMOL extension, the CLI takes a PDB or mmCIF file as input and generates a script for coloring in Chimera or PyMOL. By pasting this script into the command line of the specified viewer, users can visualize pseudoknot layers by applying colors to the structure.
Fig 2.
Examples of the structures which have non-nested interactions involving canonical base pairs and non-canonical base pairs visualized by PseudoknotVisualizer are shown.
This figure illustrates examples from PDB IDs 7PTK [27] and 6T3R [28], both of which are large sequences exceeding 300 nucleotides in length, making them particularly challenging to analyze visually without computational assistance. Note that, as demonstrated in Fig 1, all structural elements were set to white prior to applying the PseudoknotVisualizer coloring operation for clarity. These visualizations were generated with annotator=RNAView and the option include_all, thereby including the non-nested interactions involving non-canonical base pairs. The color scheme is as follows: white represents unpaired bases; gray indicates paired bases including non-canonical base pairs in the core layer; red, blue, and green represent paired bases in non-nested layers 1, 2, and 3, respectively.
Fig 3.
(a) Both graphs represent the frequency of the number of layers in RNA chains from PDB entries on the condition that these entries contain at least one base pair.
The top graph considers only canonical base pairs, showing that over 80 % of chains have at most 2 layers. The bottom graph includes all base pairs, including non-canonical ones, demonstrating a larger number of layers compared to the top graph. Nevertheless, over 80 % of chains still have at most 3 layers. (b) Distribution of canonical and non-canonical base pairs across different decomposed layers in RNA molecules that contain at least one pseudoknot or other non-nested interactions, as determined by the PseudoknotVisualizer. Results shown were obtained using DSSR as the base-pair annotator.