RNA FRABASE

RNA FRABASE provides access to a database derived from the Protein Data Bank (PDB) and pattern-based search tools for identification and conformational analysis of three-dimensional (3D) RNA structures.

Key Features:

• Database Extent: Collection of 1565 PDB-deposited RNA structures, including all Nuclear Magnetic Resonance (NMR) models.
• Search Engine Capabilities: Querying by user-defined RNA secondary structure patterns expressed in an enhanced dot-bracket notation extended to accommodate multi-stranded structures and residues with missing coordinates.
• Advanced Search Patterns: Novel algorithms enable formulation of advanced searching patterns to screen for specific tertiary structural elements and highly populated motifs.
• Conformational Analysis and Visualization: Multi-parameter conformational analyses on identified 3D RNA fragments with instant visualization of selected fragments.
• Structural Filters: "On the spot" structural filters to refine search results based on specific conformational parameters.

Scientific Applications:

• Motif Identification: Identification and comparative analysis of RNA tertiary motifs across PDB-derived structures.
• Folding Mechanisms: Analysis of conformational parameters relevant to RNA folding mechanisms.
• Interaction and Function Studies: Investigation of RNA interactions and structural features related to function.
• Cellular and Therapeutic Research: Investigation of novel RNA roles in cellular processes and potential therapeutic applications via 3D structure analysis.

Methodology:

Database compiled from PDB-deposited RNA structures including NMR models; search implemented using an enhanced dot-bracket notation extended for multi-stranded structures and residues with missing coordinates; novel algorithms support advanced pattern searches; multi-parameter conformational analyses and on-the-spot structural filters are applied, with instant visualization of identified 3D fragments.