RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures

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).