WebFR3D

WebFR3D searches and annotates atomic-resolution RNA three-dimensional (3D) structure files to identify and compare RNA structural motifs.

Key Features:

• Geometric Search Mode: Identifies motifs within RNA 3D structures that are similar to a user-defined query structure.
• Symbolic Search Mode: Locates sets of nucleotides involved in user-defined interaction patterns.
• Customizable Constraints: Supports constraints on sequence specificity, sequence continuity, base pairing, and base-stacking during searches.
• Motif Identification: Detects RNA 3D structural motifs including hairpin loops, internal loops, junction loops, sarcin-ricin loops, kink-turn internal loops, T-loops, and GNRA hairpin loops.
• Search Scope: Searches individual Protein Data Bank (PDB) files or across datasets of 3D structure files.
• Comparison Output: Produces superpositions of 3D instances and sequence alignments annotated with pairwise interactions for comparative analysis.

Scientific Applications:

• RNA structure–function analysis: Enables detailed annotation and comparison of RNA 3D structures to study structure–function relationships.
• Stability and interaction studies: Facilitates investigation of how specific structural motifs contribute to RNA stability, function, and interactions with other biomolecules.
• Evolutionary analysis: Supports exploration of evolutionary conservation of RNA motifs.
• Therapeutic and disease research: Aids design of RNA-based therapeutics and investigation of molecular mechanisms underlying RNA-related diseases.

Methodology:

Performs geometric and symbolic searches of atomic-resolution RNA 3D structures (PDB files) using user-defined query structures or interaction constraints, applies customizable constraints on sequence and interactions (sequence continuity, base pairing, base-stacking), and outputs 3D superpositions and sequence alignments annotated with pairwise interactions.