PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures

Summary: 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.Author summary: In this study, we introduce PseudoknotVisualizer, an open-source tool for direct visualization of RNA pseudoknots within three-dimensional structures. RNA pseudoknots are critical for functions such as telomerase activity and programmed ribosomal frameshifting, yet are difficult to identify and display in 3D viewers. PseudoknotVisualizer offers two user-friendly interfaces—an extension for the world’s most widely used 3D molecular graphics viewer and a command-line interface compatible with that viewer or another leading platform. Both interfaces leverage an external module that extracts base-pairing information from tertiary coordinates of RNA structures and then iteratively decomposes these base pairs into pseudoknot-free layers via dynamic programming. Each layer is assigned a unique color, enabling rapid, intuitive recognition of pseudoknot distribution in complex RNA molecules. Applying our tool to 1,915 RNA chains from the PDB revealed that canonical base pairs predominate in the core layer (87 %), while non-canonical base pairs are enriched (30 %) in the other non-nested layers; most chains exhibit no more than three layers of pseudoknots. By clarifying pseudoknot architecture in RNA 3D structures, PseudoknotVisualizer accelerates structural analysis and supports the development of computational structure prediction methods.