ARTEM

ARTEM performs topology-independent superposition of arbitrary RNA 3D structure fragments to identify and characterize long-range tertiary RNA motifs.

Key Features:

• Topology-Independent Superposition: Aligns RNA 3D fragments without relying on sequence similarity, annotated interactions, or backbone topology, assuming at least one residue-residue match with near-zero RMSD in an ideal superposition.
• Comprehensive Residue Matching: Explores all N*M single-residue matches between two structures and identifies subsets of mutually closest residues to establish optimal alignments.
• Multiple Superposition Results Ordered by Size: Produces multiple alternative superpositions and reports them ordered by size.
• Format Compatibility: Accepts and outputs PDB and mmCIF file formats.

Scientific Applications:

• Long-range tertiary interaction discovery: Enables identification and characterization of long-range tertiary RNA interactions and motifs formed between distant loops and helical regions.
• Dataset generation: Supports generation and curation of annotated long-range RNA 3D module datasets, exemplified by the LOng-RAnge RNA 3D modules (LORA) dataset.
• Motif family identification: Facilitates identification and categorization of long-range motif families, including Planar Staples, Tilted Staples, and Helical Packing Motifs.
• Interaction analysis: Reveals canonical A-minor interactions alongside previously undescribed staple interactions within RNA 3D structures.

Methodology:

Uses a novel algorithmic approach that aligns RNA 3D modules independently of annotation, sequence, and topology by exploring all N*M single-residue matches, identifying subsets of mutually closest residues, and assuming at least one residue-residue match with near-zero RMSD to establish the superposition.