TY - GEN
T1 - DegSampler
T2 - 18th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2018
AU - Maruyama, Osamu
AU - Matsuzaki, Fumiko
N1 - Funding Information:
This work was supported by JSPS KAKENHI Grant Number JP17K00407.
Publisher Copyright:
© 2018 IEEE.
PY - 2018/12/6
Y1 - 2018/12/6
N2 - 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.
AB - 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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U2 - 10.1109/BIBE.2018.00009
DO - 10.1109/BIBE.2018.00009
M3 - Conference contribution
AN - SCOPUS:85060376828
T3 - Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018
SP - 1
EP - 9
BT - Proceedings - 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering, BIBE 2018
PB - Institute of Electrical and Electronics Engineers Inc.
Y2 - 29 October 2018 through 31 October 2018
ER -