CoDNaS-RNA

CoDNaS-RNA catalogs and quantifies conformational diversity of RNA molecules by aggregating experimentally determined structures and comparing alternative conformers to support analyses of RNA structural variability and function.

Key Features:

• Comprehensive Data Collection: Aggregates RNA structures from the Protein Data Bank (wwPDB) including data derived from X‑Ray diffraction, Nuclear Magnetic Resonance (NMR), and cryo‑Electron Microscopy (cryo‑EM).
• Clustering and Comparison: Retrieves and clusters known structures to identify alternative conformers and performs pairwise structural comparisons to quantify conformational variability.
• Structural and Interaction Annotations: Provides structural feature annotations and molecular interaction data, enabling analysis of site‑specific interactions between RNA molecules and bound polynucleotides or proteins.
• Cross‑Referencing: Integrates external identifiers and annotations by cross‑referencing resources such as RNAcentral.

Scientific Applications:

• RNA dynamics and function: Systematic comparison of alternative conformers to investigate relationships between RNA structural variability and biological function.
• Modulator identification: Identification of conformational states that may inform searches for modulators of RNA structure and function.
• Interaction analysis: Exploration of site‑specific RNA interactions with polynucleotides and proteins to relate structural changes to molecular recognition and mechanism.

Methodology:

Structures are retrieved from the wwPDB (X‑Ray, NMR, cryo‑EM), clustered to identify alternative conformers per RNA molecule, and subjected to pairwise structural comparisons to measure variability, with incorporation of structural features, interaction data and cross‑references to RNAcentral.