RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.
In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbee-a new tool that allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also within protein complexes. The method works not only for first but also for high order pseudoknots, and gives an information about canonical and non-canonical base pairs. A combination of these features is unique among existing applications for RNA structure analysis. Additionally, a function of converting between the text notations, i.e. BPSEQ, CT and extended dot-bracket, is provided. In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs. RNApdbee is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/.
Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.
Maciej
M
Antczak
Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.
Tomasz
T
Zok
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Mariusz
M
Popenda
Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Piotr
P
Lukasiak
Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Ryszard W
RW
Adamiak
Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Jacek
J
Blazewicz
Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland mszachniuk@cs.put.poznan.pl.
Marta
M
Szachniuk
D020029:Base Pairing; D020407:Internet; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012984:Software
D012313:RNA