QRNAstruct

QRNAstruct extracts position-specific RNA secondary structural features and correlates them with measured bioactivity to identify structural determinants of RNA function.

Key Features:

• Position-Specific Structural Feature Calculation: Calculates position-specific structural features by enumerating all possible secondary structure configurations for each RNA sequence.
• Ridge Regression Model: Trains a Ridge regression model using extracted structural feature vectors as predictors and bioactivity values as response variables to quantify structure–activity relationships.
• Versatility Across Diverse Data Sets: Applies to datasets varying in data size, sequence length, sequence similarity, and number of RNA molecules.

Scientific Applications:

• Intramolecular Structural Analysis: Extracts intramolecular structural features from bacterial translation initiation sites and self-cleaving ribozymes.
• Intermolecular Structural Insights: Analyzes intermolecular interactions such as rRNAs with Shine-Dalgarno sequences and U1 RNAs with splicing sites.

Methodology:

Collects sequence–activity data pairs; calculates all possible secondary structures for each RNA sequence; extracts position-specific structural features from those configurations; trains a Ridge regression model correlating structural feature vectors with bioactivity values.