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. Here, we present the RNA FRABASE version 2.0, which 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.

In the 2.0 ver. database contains RNA sequences and secondary structures, described in the dot-bracket notation, derived from 2753 PDB-deposited RNA structures and their complexes. It also contains atom coordinates of the unmodified and modified nucleotide and nucleoside residues (1921887 cases) extracted from the PDB-deposited RNA structures, as well as torsion and pseudotorsion angle values, sugar pucker parameters and classification of base pair types. Also new functionalities "Structural elements" and "Secondary structures" were added.

Authors, ver.1.0
Mariusz Popenda¹, Marek Blazewicz², Marta Szachniuk², Ryszard W. Adamiak¹

1. Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, PAS, 61-704 Poznan, Poland
2. Department of Bioinformatics, Institute of Bioorganic Chemistry, PAS, 61-704 Poznan, Poland

Authors, ver. 2.0
Mariusz Popenda¹, Marta Szachniuk^2,3, Marek Blazewicz^3,4, Szymon Wasik³, Edmund K. Burke⁵, Jacek Blazewicz^2,3, Ryszard W. Adamiak¹

1. Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, PAS, 61-704 Poznan, Poland
2. Department of Bioinformatics, Institute of Bioorganic Chemistry, PAS, 61-704 Poznan, Poland
3. Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
4. Poznan Supercomputing and Networking Center, 60-529 Poznan, Poland
   
5. ASAP, School of Computer Science and IT, University of Nottingham, Nottingham, NG8 1BB, United Kingdom

Acknowledgements

The RNA FRABASE project has been supported by the Foundation for Polish Science [grant SP 01/04; 2005-2008] and the Polish Ministry of Science and Higher Education [3T09A01429, 2005-2008; PBZ-MniSW-07/I/2007/01, 2008-2010; and in part NN 519314635, 2008 - 2010]. M.B. and S.W. have been partially supported by the Erasmus fellowship at the University of Nottingham.
The authors thank the following undergraduates from Poznan University of Technology: Natalia Bartol, Karol Bonenberg, Gabriel Kaczmarek, Adam Starikiewicz, Jakub Staszak and Tomasz Zok.