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Raktim Mitra, Ari S. Cohen, Remo Rohs (Department of Quantitative & Computational Biology, University of Southern California Los Angeles, CA 90089, USA)
Analyzing and visualizing the tertiary structure and complex interactions of RNA is essential for being able to mechanistically decipher their molecular functions in vivo. Secondary structure visualization software can portray many aspects of RNA; however, these layouts are often unable to preserve topological correspondence since they do not consider tertiary interactions between regions of an RNA molecule. The RNAscape webserver produces visualizations that can preserve topological correspondence while remaining both visually intuitive and structurally insightful. RNAscape achieves this via a structural mapping algorithm which prioritizes helical segments, reflecting their tertiary organization. Non-helical segments are mapped to minimize structural clutter. RNAscape runs a plotting script designed to generate publication-quality images. RNAscape supports non-standard nucleotides, multiple base-pair annotation styles, and requires zero programming. Users can upload their own structures or enter a Protein Data Bank (PDB) ID of a structure. The webserver allows users to interact with and customize visualizations through various advanced settings. URL: https://rnascape.usc.edu/