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Journal of Biomolecular NMR

, Volume 71, Issue 1, pp 11–18 | Cite as

Application of Dirichlet process mixture model to the identification of spin systems in protein NMR spectra

  • Piotr KlukowskiEmail author
  • Michał Augoff
  • Maciej Zamorski
  • Adam Gonczarek
  • Michał J. Walczak
Article

Abstract

Analysis of structure, function and interactions of proteins by NMR spectroscopy usually requires the assignment of resonances to the corresponding nuclei in protein. This task, although automated by methods such as FLYA or PINE, is still frequently performed manually. To facilitate the manual sequence-specific chemical shift assignment of complex proteins, we propose a method based on Dirichlet process mixture model (DPMM) that performs automated matching of groups of signals observed in NMR spectra to corresponding nuclei in protein sequence. The model has been extensively tested on 80 proteins retrieved from the BMRB database and has shown superior performance to the reference method.

Keywords

Chemical shift assignment Mixture models Spin system identification 

Notes

Acknowledgements

The research has been co-financed by the Ministry of Science and Higher Education, Republic of Poland: Adam Gonczarek, Grant No. 0402/0082/17.

Author contributions

PK designed the model with the support of AG and MA; PK and MA implemented the model and the experiments; PK and MA designed the experiments; PK, MA, AG, MJW discussed the results and wrote the manuscript, MZ prepared the Dumpling components to make the model publicly available.

Supplementary material

10858_2018_185_MOESM1_ESM.pdf (5.5 mb)
Supplementary material 1 (PDF 5.51 MB)

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Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  1. 1.Faculty of Computer Science and ManagementWrocław University of Science and TechnologyWrocławPoland
  2. 2.Captor Therapeutics Ltd.WrocławPoland
  3. 3.Alphamoon Ltd.WrocławPoland

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