What we actually do

The main areas of our research are: DNA sequencing and assembling (including design of algorithms for the NGS sequencers); protein structure analysis; RNA structure analysis and prediction (including automatic tertiary structure prediction tool); nanotechnology and DNA computing.

RNA structural databases
A number of bioinformatic tools have been proposed to explore two major structural databases (PDBNDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE, a web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures.

RNA FRABASE 2.0 stores a wide selection of structural data about PDB-deposited RNA structures:
- core data: RNA sequences, secondary structures, the PDB header data (identification codes, experimental method used, resolution, PDB deposition date and number of models), the NDB identification codes);
- a collection of atom coordinates of unmodified and modified nucleotide residues occurring in RNA structures;
- a description of torsion angles and sugar pucker parameters, including values for the pseudotorsion angles;
- base-base and inter base pair parameters;
- base pair location, i.e. information specifying whether one or both bases of the pair belong to the resulting fragment;
- a complete classification of canonical and non-canonical base pair types, in both Westhof's and Saenger's notation and information about multiplets;
- information about original residue and chain numbering;
- graphical views of RNA secondary structures.

The database is served by a search engine designed to search for user-specified single- or multi-stranded RNA fragments. Search algorithms operate on the database of the RNA sequences and the library of RNA secondary structures, coded in the dot-bracket format. Due to an efficiency of the engine, RNA FRABASE is the only web-accessible tool that enables fast automatic exploration of such a substantial selection of structural parameters available for user-defined 3D RNA fragments. The tool is widely used by the researchers all over the world in the study of RNA features.

RNA FRABASE has been developed in our lab, in cooperation with a group of biochemists from the Laboratory of Structural Chemistry of Nucleic Acids, IChB PAS. The first version of the tool has been released in 2007, version 2.0 appeared in 2010. More information can be found in the following papers:

M. Popenda, M. Blazewicz, M. Szachniuk, R.W. Adamiak.
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. Nucleic Acids Research 36, 2008, D386-D391 (published online on October 5, 2007, doi:10.1093/nar/gkm786).

M. Popenda, M. Szachniuk, M. Blazewicz, S. Wasik, E.K. Burke, J. Blazewicz, R.W. Adamiak.
RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. BMC Bioinformatics, 2010, 11:231 (published online on May 6, 2010, doi:10.1186/1471-2105-11-231).