About RNApdbee

In the RNA structural biology and bioinformatics an access to correct RNA secondary structure representation is of crucial importance. This is true for both, secondary and three-dimensional RNA structure prediction studies.

Here, we present RNApdbee which greatly facilitates an access to RNA secondary structure topology extracted from PDB/mmCIF files of both, knotted and unknotted RNA structures. The tool also allows to convert between BPSEQ, CT and dot-bracket notations, and provides visualization of RNA secondary structures.


Maciej Antczak1, Tomasz Zok1, Mariusz Popenda2, Michal Zurkowski1, Piotr Lukasiak1,2, Ryszard W. Adamiak1,2, Jacek Blazewicz1,2, Marta Szachniuk1,2

  1. Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan Poland
  2. Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland

Acknowledgements and Funding

RNApdbee project has been supported by the National Science Centre, Poland, under the following grants: MAESTRO 2012/06/A/ST6/00384 (2013-2016), OPUS 2016/23/B/ST6/03931 (2017-2020), PRELUDIUM 2016/23/N/ST6/03779 (2017-2018).