PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures

We introduce the PseudoknotVisualizer, a specialized software designed to identify and visualize pseudoknots within RNA three-dimensional structures. Typically, RNA secondary structures containing pseudoknots can be decomposed into multiple pseudoknot-free layers. Our software colors the base pairs in each pseudoknot layer, enabling the visualization of pseudoknot distribution within three-dimensional structures. Specifically, users can utilize the PseudoknotVisualizer as a PyMOL extension, applying it directly to RNA molecules loaded in PyMOL. Additionally, a Command Line Interface (CLI) is provided, allowing users to generate coloring commands in Chimera or PyMOL formats, which can then be manually copied and pasted for visualization. By facilitating the clear depiction of pseudoknots in RNA tertiary structures, this tool addresses significant challenges in the identification and visualization of pseudoknots in RNA structural analysis, thereby enhancing research productivity and expanding potential applications in molecular biology. Availability and implementation: PseudoknotVisualizer is freely available at https://github.com/TakumiOtagaki/PseudoknotVisualizer.