RNA Bricks—a database of RNA 3D motifs and their interactions

摘要: The RNA Bricks database (http://iimcb.genesilico.pl/rnabricks), stores information about recurrent 3D motifs and their interactions, found in experimentally determined structures RNA-protein complexes. In contrast to other similar tools (RNA Motif Atlas, Frabase, Rloom) motifs, i.e. 'RNA bricks' are presented the molecular environment, which they were determined, including RNA, protein, metal ions, water molecules ligands. All nucleotide residues bricks annotated with structural quality scores that describe real-space correlation coefficients electron density data (if available), backbone geometry possible steric conflicts, can be used identify poorly modeled residues. is also equipped an algorithm for motif search comparison. compares spatial positions of atoms user-provided query structure stored without relying on sequence or secondary information. This enables identification local similarities among evolutionarily related unrelated molecules. Besides, utility searching according similarity, makes it modified ribonucleotide at specific positions.