Nucleic Acids Research Advance Access originally published online on October 5, 2007
Nucleic Acids Research 2008 36(Database issue):D386-D391; doi:10.1093/nar/gkm786
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Nucleic Acids Research, 2008, Vol. 36, Database issue D386-D391
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures
a
ewicz2
1Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Pozna
, 2Institute of Computing Science, Pozna University of Technology, Piotrowo 2, 60-965 Pozna and 3Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Pozna, Poland
*To whom correspondence should be addressed. Tel: +48 61 8528503; Fax: +48 61 8520532; Email: adamiakr{at}ibch.poznan.pl
Received August 12, 2007. Revised September 15, 2007. Accepted September 17, 2007.
The RNA FRABASE is a web-accessible engine with a relational database, which allows for the automatic search of user-defined, 3D RNA fragments within a set of RNA structures. This is a new tool to search and analyse RNA structures, directed at the 3D structure modelling. The user needs to input either RNA sequence(s) and/or secondary structure(s) given in a ‘dot-bracket’ notation. The algorithm searching for the requested 3D RNA fragments is very efficient. As of August 2007, the database contains: (i) RNA sequences and secondary structures, in the ‘dot-bracket’ notation, derived from 1065 protein data bank (PDB)-deposited RNA structures and their complexes, (ii) a collection of atom coordinates of unmodified and modified nucleotide residues occurring in RNA structures, (iii) calculated RNA torsion angles and sugar pucker parameters and (iv) information about base pairs. Advanced query involves filters sensitive to: modified residue contents, experimental method used and limits of conformational parameters. The output list of query-matching RNA fragments gives access to their coordinates in the PDB-format files, ready for direct download and visualization, conformational parameters and information about base pairs. The RNA FRABASE is automatically, monthly updated and is freely accessible at http://rnafrabase.ibch.poznan.pl (mirror at http://cerber.cs.put.poznan.pl/rnadb).