The function of RNA is strongly associated with its structure, therefore an appropriate recognition of the latter, on every level of organization, is of great importance. It particularly concerns the assessment of base-base interactions, described as the secondary structure, the knowledge of which contributes to an interpretation of RNA functions. It also allows for structural analysis on the three-dimensional level. The secondary structure of RNA molecules can be predicted from sequence using in
silico methods often adjusted with experimental data, or derived upon 3D structure atom coordinates. In both cases, computational approaches consider mostly Watson-Crick and wobble base pairs to describe the
structure. Handling of non-canonical interactions, important for a full description of RNA structure, is still found challenging.
Here, we introduce RNApdbee that supports processing of RNA structures, also within protein complexes. The method allows to work with unknotted and knotted RNAs, and is able to classify pseudoknot
orders. It gives an information about extended secondary structure characterized by canonical and non-canonical base pairs. We also present the novel protocol for assessing an extended RNA secondary
structure upon RNA sequence. Its idea is based on predicting the RNA 3D structure from user-provided sequence and next, assessing the extended secondary structure from foreseen atom coordinates. Our example implementation of the protocol involves RNAComposer for the 3D RNA structure prediction and RNApdbee for base pair annotation. This example performance reveals better accuracy in non-canonical base pair assessment than the compared methods that directly predict RNA secondary structure. Both webserver tools involved in the protocol are freely available to all users and can be accessed at:
http://rnapdbee.cs.put.poznan.pl/ (RNApdbee) and http://rnacomposer.cs.put.poznan.pl/ (RNAComposer).
Acknowledgements: The authors acknowledge support from National Science Centre, Poland (2012/05/B/ST6/03026, 2012/06/A/ST6/00384).
- M. Antczak, T. Zok, M. Popenda, P. Lukasiak, R.W. Adamiak, J. Blazewicz, M. Szachniuk. RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs, Nucleic Acids Research 42(W1), 2014, W368-W372.
- M. Popenda, M. Szachniuk, M. Antczak, K.J. Purzycka, P. Lukasiak, N. Bartol, J. Blazewicz, R.W. Adamiak. Automated 3D structure composition for large RNAs, Nucleic Acids Research 40(14), 2012, e112.