MLP accompanied beam search for the resonance assignment problem
- 239 Downloads
Resonance signal assignment is a well known problem encountered during the process of biomolecule structure determination based on nuclear magnetic resonance (NMR) spectroscopy. As one of the first steps following the experimental part of the process, it significantly affects the quality of a resulting molecule model. In the paper we present a new approach for automated signal assignment in two-dimensional NMR spectra of RNA molecules. The proposed algorithm combines beam search with a neural network in order to reconstruct and evaluate solutions. Computational tests with a set of experimental and simulated NMR spectra show an excellent performance of the approach in comparison with the existing methods. The algorithm implementation is freely available at http://www.cs.put.poznan.pl/mszachniuk/bsmlp.zip.
KeywordsBeam search Neural network RNA assignment NMR
This research has been supported by grants from the Ministry of Science and Higher Education and from the National Science Centre, Poland (2012/05/B/ ST6/03026). We also acknowledge the support from the Erasmus fellowship to M.M. at the University of Siegen. The authors thank dr Lukasz Popenda from NanoBioMedical Centre, Adam Mickiewicz University (Poznan, Poland) for providing spectral data for computational experiments. We also wish to thank the anonymous referees for their thorough reviews, which made us significantly improve the quality of this publication.
- Blazewicz, J., Szachniuk, M., Wojtowicz, A.: Evolutionary approach to NOE paths assignment in RNA structure elucidation. IEEE CIBCB Proceedings 206–213 (2004)Google Scholar
- Blazewicz, J., Szachniuk, M., Wojtowicz, A.: Evolutionary algorithm for a reconstruction of NOE paths in NMR spectra of RNA chains. Bull. Pol. Acad. Sci. Tech. Sci. 52, 221–230 (2004)Google Scholar
- Gdaniec, Z., Popenda, M., Popenda, L.: Personal commmunication (2005)Google Scholar
- Lowerre, B.T.: The HARPY speech recognition system. Ph.D. thesis, Carnegie-Mellon University, USA (1976)Google Scholar
- Szachniuk, M.: Combinatorial analysis of 2D-NOESY spectra in nuclear magnetic resonance spectroscopy of RNA molecules. Ph.D. thesis, Poznan University of Technology, Poland (2005)Google Scholar