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Development of machine learning algorithms for the prediction of terpene synthase activity

  • Full or part time
    Dr T Pluskal
  • Application Deadline
    Sunday, February 23, 2020
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

Bioactive plant metabolites are an essential source of chemical scaffolds for the development of new medicines. Our group is interested in establishing new cutting-edge methods to harness the biosynthetic potential of plant specialized metabolism for the benefit of human health. One of the interesting problems is prediction of enzyme activity from its amino acid sequence using computational approaches. In this project, we will develop machine learning platforms (e.g., deep neural networks) for predicting the chemical structures produced by a specific class of plant metabolic enzymes, terpene synthases. These enzymes are collectively responsible for generating the largest and the most diverse family of plant specialized metabolites with numerous medical and industrial applications. As side projects, the student will contribute to the development of computational workflows for mass spectrometry, metabolomics, molecular networking, and de novo transcriptome sequencing.

How to apply

To apply for a PhD study at IOCB Prague, you must hold a Master’s degree (MSc) or the equivalent of the MSc in similar field (four or five year undergraduate degree). The application can be submitted before obtaining the Master’s degree, however, the applicant should obtain the degree within five months after the application deadline.

For more information visit our website “Call for PhD applications 2020”:
https://www.uochb.cz/en/phd-program

If you decided to apply, please do so online via our application form:
https://www.uochb.cz/en/call-for-phd-applications

Funding Notes

Regular monthly income of students at IOCB Prague varies depending on the faculty scholarship and supervisor's financial options.

References

Christianson, D. W. Structural and Chemical Biology of Terpenoid Cyclases. Chem. Rev. 117, 11570–11648 (2017)

Vattekkatte, A., Garms, S., Brandt, W. & Boland, W. Enhanced structural diversity in terpenoid biosynthesis: enzymes, substrates and cofactors. Org. Biomol. Chem. 16, 348–362 (2018)

Related Subjects



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