RNA CoSSMos

RNA CoSSMos catalogs RNA secondary structure motifs from Protein Data Bank (PDB) entries, providing detailed structural annotations for internal loops, bulge loops, and hairpin loops.

Key Features:

• Secondary Structure Motif Database: Extracts and annotates internal loops, bulge loops, and hairpin loops from 2156 PDB files, documenting sugar pucker conformations, glycosidic bond types, hydrogen bonding patterns, and base stacking interactions.
• Curated Structural Validation: Applies systematic identification, reclassification, and removal of false positives to ensure accurate motif annotation.
• Advanced Query System: Enables searches using PDB metadata, experimental parameters, sequence information, motif types, and structural features for targeted motif retrieval.

Scientific Applications:

• RNA Structural Analysis: Supports investigation of RNA secondary structure motifs for RNA tertiary structure prediction, protein–RNA interaction studies, and RNA-based therapeutic design.

Methodology:

RNA CoSSMos systematically parses PDB structures to identify predefined RNA loop motifs, extracts detailed conformational and interaction parameters, curates entries to eliminate false positives, and organizes validated structural data for motif-specific retrieval and comparative analysis.