RNA Bricks--a database of RNA 3D motifs and their interactions.
The RNA Bricks database (http://iimcb.genesilico.pl/rnabricks), stores information about recurrent RNA 3D motifs and their interactions, found in experimentally determined RNA structures and in RNA-protein complexes. In contrast to other similar tools (RNA 3D Motif Atlas, RNA Frabase, Rloom) RNA motifs, i.e. 'RNA bricks' are presented in the molecular environment, in which they were determined, including RNA, protein, metal ions, water molecules and ligands. All nucleotide residues in RNA bricks are annotated with structural quality scores that describe real-space correlation coefficients with the electron density data (if available), backbone geometry and possible steric conflicts, which can be used to identify poorly modeled residues. The database is also equipped with an algorithm for 3D motif search and comparison. The algorithm compares spatial positions of backbone atoms of the user-provided query structure and of stored RNA motifs, without relying on sequence or secondary structure information. This enables the identification of local structural similarities among evolutionarily related and unrelated RNA molecules. Besides, the search utility enables searching 'RNA bricks' according to sequence similarity, and makes it possible to identify motifs with modified ribonucleotide residues at specific positions.
International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland and Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland.
Grzegorz
G
Chojnowski
Tomasz
T
Walen
Janusz M
JM
Bujnicki
D000465:Algorithms; D030561:Databases, Nucleic Acid; D020407:Internet; D008024:Ligands; D008670:Metals / Q000737:chemistry; D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000737:chemistry; D014867:Water / Q000737:chemistry
D008024:Ligands; D008670:Metals; D016601:RNA-Binding Proteins; D014867:Water; D012313:RNA