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URL: http://rnafrabase.ibch.poznan.pl/
Proper Citation: RNA FRABASE - RNA FRAgments search engine and dataBASE (RRID:SCR_012808)
Description: Engine and database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation. The database contains RNA sequences and secondary structures, described in the dot-bracket notation, derived from PDB-deposited RNA structures and their complexes. It also contains atom coordinates of the unmodified and modified nucleotide and nucleoside residues extracted from the PDB-deposited RNA structures, as well as torsion and pseudotorsion angle values, sugar pucker parameters and classification of base pair types given for the PBD-deposited RNA structures. Knowledge of the three dimensional RNA structure is crucial for all fields of biomolecular research. In contrast to the protein field, only about 1.300 experimentally derived structures of RNAs are deposited in the Protein Data Bank (PDB). To complement the results of experimental studies, new approaches based on bioinformatics and calculation are pursued in several laboratories to make tertiary RNA structure prediction possible. RNA FRABASE version 2.0 should greatly facilitate various RNA structure modelling approaches, RNA structure analysis and motif searching. If one compares the three dimensional RNA structure to a spatial puzzle, the RNA FRABASE allows to pull out a defined piece of this puzzle - the 3D RNA fragment. The architecture of the web-accessible RNA FRABASE engine and database is based on the following information path: PDB-deposited RNA structures �� RNA sequences and secondary structures described in the dot-bracket notation �� secondary structures of RNA fragments �� 3D RNA fragments. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide on the spot structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided.
Abbreviations: RNA FRABASE
Synonyms: RNA FRAgments search engine dataBASE, RNA FRAgments search engine and dataBASE, RNA FRABASE - RNA FRAgments search engine dataBASE
Resource Type: d spatial image, data or information resource, analysis service resource, service resource, production service resource, database, data analysis service
Defining Citation: PMID:20459631, PMID:17921499
Keywords: structural element, secondary structure, rna, rna structure, 3d rna fragment, bio.tools
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