NDB Tools

NDB Tools provide classification and visualization of RNA structures to analyze base-pair interactions and recurrent three-dimensional motifs.

Key Features:

• BPViewer: Displays three-dimensional coordinates of individual or collections of base pairs within RNA structures to represent spatial arrangements and interactions.
• RNAview: Automatically identifies and classifies base pairs formed by combinations of the Watson-Crick, Hoogsteen, and Sugar edges and generates two-dimensional diagrams in Postscript, VRML, and RNAML formats representing secondary and tertiary structure.
• RNAMLview: Rearranges regions of RNAview two-dimensional diagrams while maintaining links among helices and single strands to produce standard or custom layouts such as tRNA cloverleafs.
• Classification System: Implements a nomenclature classifying base pairs by planar edge-to-edge interactions (Watson-Crick, Hoogsteen, Sugar) and cis/trans orientations, defining 12 basic geometric types with at least two hydrogen bonds.
• Graphical Conventions: Specifies conventions for depicting non-Watson-Crick interactions on secondary-structure diagrams to highlight isosteric relationships and recurrent three-dimensional motifs.

Scientific Applications:

• RNA Structure Analysis: Identifies and classifies RNA motifs and base-pairing patterns to support studies of RNA-RNA self-assembly and RNA-protein interactions.
• Homology Modeling: Uses the base-pair classification system to aid homology modeling and comparison of RNA tertiary motifs with known structures.
• Data Survey and Statistics: Provides statistics on the occurrence of base-pair edges and families derived from a survey of 41 unique structures in the NDB.

Methodology:

The tools apply symbolic conventions for base-pair interactions to enable automated annotation and classification and provide high-resolution geometric examples for depiction and analysis.