Application of Dirichlet process mixture model to the identification of spin systems in protein NMR spectra
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.
KeywordsChemical shift assignment Mixture models Spin system identification
The research has been co-financed by the Ministry of Science and Higher Education, Republic of Poland: Adam Gonczarek, Grant No. 0402/0082/17.
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.
- Attias H (2000) A variational Bayesian framework for graphical models. In: Advances in Neural Information Processing Systems, pp 209–215Google Scholar
- Grzesiek S, Bax A (1993) Amino acid type determination in the sequential assignment procedure of uniformly 13 C/15 N-enriched proteins. J Biomol NMR 3:185–204Google Scholar
- Güntert P (2004) Automated NMR structure calculation with cyana. In: Downing AK (ed) Protein NMR techniques. Humana Press, Totowa, pp 353–378Google Scholar
- Jones E, Oliphant T, Peterson P et al (2001) SciPy: open source scientific tools for Python. URL http://www.scipy.org/
- Rieping W, Vranken WF (2010) Validation of archived chemical shifts through atomic coordinates. Proteins 78:2482–2489Google Scholar
- Rule GS, Hitchens TK (2006) Fundamentals of protein NMR spectroscopy. Springer Science & Business Media, New YorkGoogle Scholar
- Wang B, Wang Y, Wishart D (2010) A probabilistic approach for validating protein NMR chemical shift assignments. J Mol Biol 47:85–99Google Scholar