RNApdbee 3.0: A unified web server for comprehensive RNA secondary structure annotation from 3D coordinates

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.