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