ARTEM

ARTEM is a tool for the superposition of two arbitrary RNA 3D structure fragments. ARTEM doesn’t rely on sequence similarity, annotated interactions, or backbone topology. Instead, ARTEM assumes at least one residue-residue match has a close-to-zero RMSD in the ideal superposition. Then, ARTEM tries all N*M single-residue matches and derives a subset of mutually closest residues as the matches for each of the single-residue-based superpositions. Finally, ARTEM returns the superpositions ordered by their size, letting the user choose the best one based on any specific requirements. ARTEM can read/write both PDB and mmCIF format.