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MLP accompanied beam search for the resonance assignment problem

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Abstract

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.

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Acknowledgments

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.

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Authors and Affiliations

  1. Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12, 61-704 , Poznan, Poland

    Marta Szachniuk & Jacek Blazewicz

  2. Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 , Poznan, Poland

    Marta Szachniuk, Mikolaj Malaczynski & Jacek Blazewicz

  3. Department of Management and Information Sciences, University of Siegen, Hoelderlinstrasse 3, 57068 , Siegen, Germany

    Erwin Pesch

  4. University of Stirling, Stirling, Scotland, FK9 4LA, UK

    Edmund K. Burke

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  1. Marta Szachniuk
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  2. Mikolaj Malaczynski
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  3. Erwin Pesch
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  4. Edmund K. Burke
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  5. Jacek Blazewicz
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Correspondence to Marta Szachniuk.

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Szachniuk, M., Malaczynski, M., Pesch, E. et al. MLP accompanied beam search for the resonance assignment problem. J Heuristics 19, 443–464 (2013). https://doi.org/10.1007/s10732-013-9220-3

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  • DOI: https://doi.org/10.1007/s10732-013-9220-3

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