FASTR3D

FASTR3D searches the Protein Data Bank (PDB) for RNAs structurally similar to user-provided queries, enabling comparative analyses of RNA tertiary and secondary structures and primary sequences.

Key Features:

• Query Flexibility: Accepts three input types: a PDB code for an RNA tertiary structure (optionally with a residue range), an RNA secondary structure in dot-bracket notation (optionally with a primary sequence), and an RNA primary sequence in FASTA format.
• Advanced Filtering Options: Filters search results by PDB release date and by experimental method and resolution of RNA structures.
• Comprehensive Output: Returns a list of structurally similar RNAs and computes structural superposition for queries provided as tertiary structures.

Scientific Applications:

• Homology Identification: Detects homologous RNA structures to support inference of shared functional properties or evolutionary relationships.
• Structural Diversity Analysis: Enables examination of RNA tertiary-structure diversity across specified PDB release dates or experimental methods and resolutions.
• Motif and Structure–Function Exploration: Facilitates comparison of structural motifs across RNA molecules to inform structure–function relationships.

Methodology:

Performs rapid searches of the Protein Data Bank (PDB) using algorithms that compare RNA tertiary structures, dot-bracket secondary structures, and primary sequences, and computes structural superposition for tertiary-structure queries.