SCOR

SCOR classifies RNA motif structures, tertiary interactions, and interrelationships to support analysis of RNA structure-function relationships.

Key Features:

• Version and classification: SCOR 2.0 implements a classification organized as a Directed Acyclic Graph (DAG) that permits nodes to have multiple parent nodes, replacing the strictly hierarchical model of SCOR 1.2.
• Experimental sources and repository entries: As of May 15, 2003, SCOR 2.0 includes 511 RNA entries from the Protein Data Bank (PDB) comprising 5880 secondary structural elements, including 2104 hairpin loops and 3776 internal loops.
• Structural data origins: Entries are derived from NMR and X-ray crystallography studies.
• Query support: Supports queries by PDB or NDB identifiers, nucleotide sequences, and keywords.
• Data export: Provides parseable XML files containing all relevant data.
• Motif integration: Integrates well-characterized RNA motifs reported in the literature, including 'Kink turn' and 'GNRA loops', with definitions and descriptions.
• Functional and tertiary classification: Organizes RNA structures into functional groups and includes a classification of tertiary interactions observed in larger RNA structures.

Scientific Applications:

• RNA motif characterization: Analysis and comparison of RNA motif structures such as hairpin and internal loops using curated structural entries.
• Tertiary interaction studies: Examination and classification of tertiary interactions in larger RNA architectures.
• Structure-function investigations: Support for studies linking RNA structural motifs and tertiary organization to functional groupings.
• Motif reference and annotation: Reference resource for literature-defined motifs (e.g., 'Kink turn', 'GNRA loops') and their structural definitions.

Methodology:

Classification implemented as a Directed Acyclic Graph (DAG) allowing multiple parent nodes; supports queries by PDB/NDB identifiers, nucleotide sequences, and keywords; provides parseable XML files of the data.