DegSampler

Collapsed Gibbs sampler for detecting E3 binding sites

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

Abstract

In this paper, we address the problem of finding sequence motifs in substrate proteins specific to E3 ubiquitin ligases (E3s). We formulated a posterior probability distribution of sites by designing a likelihood function based on amino acid indexing and a prior distribution based on the disorderness of protein sequences. These designs are derived from known characteristics of E3 binding sites in substrate proteins. Then, we devise a collapsed Gibbs sampling algorithm for the posterior probability distribution called DegSampler. We performed computational experiments using 36 sets of substrate proteins specific to E3s and compared the performance of DegSampler with those of popular motif finders, MEME and GLAM2. The results showed that DegSampler was superior to the others in finding E3 binding motifs. Thus, DegSampler is a promising tool for finding E3 motifs in substrate proteins.

Original languageEnglish
Title of host publicationProceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1-9
Number of pages9
ISBN (Electronic)9781538662168
DOIs
Publication statusPublished - Dec 6 2018
Event18th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2018 - Taichung, Taiwan, Province of China
Duration: Oct 29 2018Oct 31 2018

Publication series

NameProceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018

Other

Other18th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2018
CountryTaiwan, Province of China
CityTaichung
Period10/29/1810/31/18

Fingerprint

Binding sites
Binding Sites
Proteins
Substrates
Probability distributions
Likelihood Functions
Ubiquitin-Protein Ligases
Amino acids
Sampling
Amino Acids
Experiments

All Science Journal Classification (ASJC) codes

  • Genetics(clinical)
  • Health Informatics
  • Oncology
  • Biomedical Engineering
  • Cardiology and Cardiovascular Medicine

Cite this

Maruyama, O., & Matsuzaki, F. (2018). DegSampler: Collapsed Gibbs sampler for detecting E3 binding sites. In Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018 (pp. 1-9). [8567448] (Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBE.2018.00009

DegSampler : Collapsed Gibbs sampler for detecting E3 binding sites. / Maruyama, Osamu; Matsuzaki, Fumiko.

Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018. Institute of Electrical and Electronics Engineers Inc., 2018. p. 1-9 8567448 (Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018).

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

Maruyama, O & Matsuzaki, F 2018, DegSampler: Collapsed Gibbs sampler for detecting E3 binding sites. in Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018., 8567448, Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018, Institute of Electrical and Electronics Engineers Inc., pp. 1-9, 18th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2018, Taichung, Taiwan, Province of China, 10/29/18. https://doi.org/10.1109/BIBE.2018.00009
Maruyama O, Matsuzaki F. DegSampler: Collapsed Gibbs sampler for detecting E3 binding sites. In Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018. Institute of Electrical and Electronics Engineers Inc. 2018. p. 1-9. 8567448. (Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018). https://doi.org/10.1109/BIBE.2018.00009
Maruyama, Osamu ; Matsuzaki, Fumiko. / DegSampler : Collapsed Gibbs sampler for detecting E3 binding sites. Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018. Institute of Electrical and Electronics Engineers Inc., 2018. pp. 1-9 (Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018).
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