DegSampler: Collapsed Gibbs Sampler for Detecting E3 Binding Sites

Research output: Contribution to conferencePaper

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
Pages1-9
Number of pages9
Publication statusPublished - Dec 10 2018
Event2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE) -
Duration: Oct 29 2018Oct 31 2018

Conference

Conference2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE)
Period10/29/1810/31/18

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samplers
binding sites
probability distribution
proteins
ubiquitin-protein ligase
amino acid sequences
amino acids
sampling

Cite this

Maruyama, O., & Matsuzaki, F. (2018). DegSampler: Collapsed Gibbs Sampler for Detecting E3 Binding Sites. 1-9. Paper presented at 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE), .

DegSampler: Collapsed Gibbs Sampler for Detecting E3 Binding Sites. / Maruyama, Osamu; Matsuzaki, Fumiko.

2018. 1-9 Paper presented at 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE), .

Research output: Contribution to conferencePaper

Maruyama, O & Matsuzaki, F 2018, 'DegSampler: Collapsed Gibbs Sampler for Detecting E3 Binding Sites' Paper presented at 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE), 10/29/18 - 10/31/18, pp. 1-9.
Maruyama O, Matsuzaki F. DegSampler: Collapsed Gibbs Sampler for Detecting E3 Binding Sites. 2018. Paper presented at 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE), .
Maruyama, Osamu ; Matsuzaki, Fumiko. / DegSampler: Collapsed Gibbs Sampler for Detecting E3 Binding Sites. Paper presented at 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE), .9 p.
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