CSSR

CSSR assigns secondary structure to coarse-grained RNA tertiary models to determine RNA secondary structure (rSS) when nucleobase atomic positions are incomplete or missing.

Key Features:

• rSS assignment: Assigns secondary structure to coarse-grained RNA tertiary models.
• Partial-atom compatibility: Operates when nucleobase atomic positions are incomplete or missing.
• Single-backbone-atom operation: Can assign rSS from models where only one backbone atom per nucleotide is known.
• Robust accuracy: Achieves approximately 90% rSS assignment accuracy under conditions of limited atomic detail.
• Extended applicability: Enables analysis of experimentally determined and computationally predicted RNA 3D structures without full atomic resolution.
• Overcomes traditional constraints: Addresses limitations of rSS assignment programs that require complete atomic structures.

Scientific Applications:

• Low-resolution cryo-EM models: Supports secondary structure assignment for RNA structures derived from cryo-electron microscopy that often provide lower-resolution models.
• Computational structure analysis: Enables analysis of computationally predicted RNA structures lacking full atomic detail.
• Functional and dynamic interpretation: Facilitates interpretation of RNA function and dynamics from coarse-grained 3D data.
• Therapeutics and diagnostics design: Aids interpretation of structural data that inform the design of RNA-based therapeutics and diagnostics.
• Research domains: Supports applications in molecular biology, genetics, and bioinformatics.

Methodology:

The algorithm assigns rSS from coarse-grained RNA tertiary models using partial atomic information and attains approximately 90% assignment accuracy under limited atomic detail.