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Updated: Apr 11, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
RNApdbee 3.0: A unified web server for comprehensive RNA secondary structure annotation from 3D coordinates
Jan Pielesiak1, Kamil Niznik1, Pawel Snioszek1
1Institute of Computing Science, Poznan University of Technology, ul. Jacka Rychlewskiego 1, 61-131 Poznan, Poland.
Abstract:
RNApdbee 3.0 (publicly available at https://rnapdbee.cs.put.poznan.pl/) offers an advanced pipeline for comprehensive RNA structural annotation, integrating 2D and 3D data to build detailed nucleotide interaction networks. It classifies base pairs as canonical or noncanonical using the Leontis-Westhof and Saenger schemes and identifies stacking, base-ribose, base-phosphate, and base-triple interactions. The tool handles incomplete or modified residues, marking missing nucleotides and distinguishing noncanonical base pairs for accurate and effective visualization. Results are provided in standard formats - namely, extended dot-bracket notation, BPSEQ, and CT - and in detailed graphical visualizations. RNApdbee decomposes 2D structures into stems, loops, and single strands and offers flexible pseudoknot encoding. Its unified framework addresses inconsistencies across structural data formats by standardizing all inputs to PDBx/mmCIF and integrating seven widely used annotation tools. Finally, RNApdbee ensures reliable, format-independent, and comprehensive RNA structural annotation and interpretation.
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