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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.

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|April 9, 2026
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Summary

RNApdbee 3.0 provides comprehensive RNA structural annotation by integrating 2D and 3D data to map nucleotide interactions. This tool ensures reliable and format-independent interpretation of RNA structures.

Keywords:
2D structure visualizationRNA 2D structure annotationRNA 3D structure processingbase-pair identificationconsensus 2D structure

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Accurate RNA structural annotation is crucial for understanding RNA function.
  • Existing tools often struggle with data inconsistencies and diverse formats.
  • A unified approach is needed for comprehensive RNA structural analysis.

Purpose of the Study:

  • To introduce RNApdbee 3.0, an advanced pipeline for RNA structural annotation.
  • To integrate 2D and 3D structural data for detailed nucleotide interaction networks.
  • To provide a reliable, format-independent tool for RNA structural interpretation.

Main Methods:

  • RNApdbee 3.0 integrates seven annotation tools and standardizes input to PDBx/mmCIF.
  • It classifies base pairs using Leontis-Westhof and Saenger schemes (canonical/noncanonical).
  • Identifies stacking, base-ribose, base-phosphate, and base-triple interactions, handling modified residues.

Main Results:

  • RNApdbee 3.0 generates detailed nucleotide interaction networks from integrated 2D and 3D data.
  • It provides results in standard formats (dot-bracket, BPSEQ, CT) and graphical visualizations.
  • The tool accurately visualizes incomplete or modified residues and noncanonical base pairs.

Conclusions:

  • RNApdbee 3.0 offers a unified framework for consistent and comprehensive RNA structural annotation.
  • It effectively addresses inconsistencies across various structural data formats.
  • The pipeline ensures reliable, format-independent RNA structural interpretation and visualization.