DegSampler: Collapsed Gibbs Sampler for Detecting E3 Binding Sites

研究成果: 会議への寄与タイプ論文

抄録

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.
元の言語英語
ページ1-9
ページ数9
出版物ステータス出版済み - 12 10 2018
イベント2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE) -
継続期間: 10 29 201810 31 2018

会議

会議2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE)
期間10/29/1810/31/18

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

これを引用

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

研究成果: 会議への寄与タイプ論文

Maruyama, O & Matsuzaki, F 2018, 'DegSampler: Collapsed Gibbs Sampler for Detecting E3 Binding Sites' 論文発表場所 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. 論文発表場所 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE), .
Maruyama, Osamu ; Matsuzaki, Fumiko. / DegSampler: Collapsed Gibbs Sampler for Detecting E3 Binding Sites. 論文発表場所 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE), .9 p.
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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.",
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