DegSampler3: Pairwise dependency model in degradation motif site prediction of substrate protein sequences

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

In the ubiquitin-proteasome system, E3 ubiquitin ligase (E3s for short) selectively recognize and bind specific regions of their substrate proteins. Sequence motifs whose sites are bound by E3 ubiquitin ligases are called degrons. Because much remains unclear about the relationship between substrate proteins of E3s and their binding sites, there is a need to computationally identify such binding sites from the substrate proteins. For this motif identification problem, in our previous works, we have proposed a series of collapsed Gibbs sampling algorithms, called DegSampler1 and DegSampler2, both of which use position-specific prior information. In this work, we propose a new collapsed Gibbs sampling algorithm, called DegSampler3, by integrating intra-motif pair-wise dependency model into the posterior probability distribution of DegSampler2. In our preliminary experiments, we found that DegSampler3 has the ability of finding more various degron sites than DegSampler2 while keeping the prediction accuracy almost the same as that of the previous method, DegSampler2.

Original languageEnglish
Title of host publicationProceedings - 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering, BIBE 2019
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages11-17
Number of pages7
ISBN (Electronic)9781728146171
DOIs
Publication statusPublished - Oct 2019
Event19th International Conference on Bioinformatics and Bioengineering, BIBE 2019 - Athens, Greece
Duration: Oct 28 2019Oct 30 2019

Publication series

NameProceedings - 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering, BIBE 2019

Conference

Conference19th International Conference on Bioinformatics and Bioengineering, BIBE 2019
CountryGreece
CityAthens
Period10/28/1910/30/19

All Science Journal Classification (ASJC) codes

  • Information Systems
  • Biomedical Engineering
  • Health Informatics

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  • Cite this

    Maruyama, O., & Matsuzaki, F. (2019). DegSampler3: Pairwise dependency model in degradation motif site prediction of substrate protein sequences. In Proceedings - 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering, BIBE 2019 (pp. 11-17). [8941973] (Proceedings - 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering, BIBE 2019). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBE.2019.00012