Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs.

As one of the most important reversible protein post-translation modifications, ubiquitination has been reported to be involved in lots of biological processes and closely implicated with various diseases. To fully decipher the molecular mechanisms of ubiquitination-related biological processes, an...

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Autores principales:	Zhen Chen, Yong-Zi Chen, Xiao-Feng Wang, Chuan Wang, Ren-Xiang Yan, Ziding Zhang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ff96e5d1d0544d5ca0936e5fe74def59
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spelling	oai:doaj.org-article:ff96e5d1d0544d5ca0936e5fe74def592021-11-18T06:48:59ZPrediction of ubiquitination sites by using the composition of k-spaced amino acid pairs.1932-620310.1371/journal.pone.0022930https://doaj.org/article/ff96e5d1d0544d5ca0936e5fe74def592011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21829559/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203As one of the most important reversible protein post-translation modifications, ubiquitination has been reported to be involved in lots of biological processes and closely implicated with various diseases. To fully decipher the molecular mechanisms of ubiquitination-related biological processes, an initial but crucial step is the recognition of ubiquitylated substrates and the corresponding ubiquitination sites. Here, a new bioinformatics tool named CKSAAP_UbSite was developed to predict ubiquitination sites from protein sequences. With the assistance of Support Vector Machine (SVM), the highlight of CKSAAP_UbSite is to employ the composition of k-spaced amino acid pairs surrounding a query site (i.e. any lysine in a query sequence) as input. When trained and tested in the dataset of yeast ubiquitination sites (Radivojac et al, Proteins, 2010, 78: 365-380), a 100-fold cross-validation on a 1∶1 ratio of positive and negative samples revealed that the accuracy and MCC of CKSAAP_UbSite reached 73.40% and 0.4694, respectively. The proposed CKSAAP_UbSite has also been intensively benchmarked to exhibit better performance than some existing predictors, suggesting that it can be served as a useful tool to the community. Currently, CKSAAP_UbSite is freely accessible at http://protein.cau.edu.cn/cksaap_ubsite/. Moreover, we also found that the sequence patterns around ubiquitination sites are not conserved across different species. To ensure a reasonable prediction performance, the application of the current CKSAAP_UbSite should be limited to the proteome of yeast.Zhen ChenYong-Zi ChenXiao-Feng WangChuan WangRen-Xiang YanZiding ZhangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 7, p e22930 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Zhen Chen Yong-Zi Chen Xiao-Feng Wang Chuan Wang Ren-Xiang Yan Ziding Zhang Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs.
description	As one of the most important reversible protein post-translation modifications, ubiquitination has been reported to be involved in lots of biological processes and closely implicated with various diseases. To fully decipher the molecular mechanisms of ubiquitination-related biological processes, an initial but crucial step is the recognition of ubiquitylated substrates and the corresponding ubiquitination sites. Here, a new bioinformatics tool named CKSAAP_UbSite was developed to predict ubiquitination sites from protein sequences. With the assistance of Support Vector Machine (SVM), the highlight of CKSAAP_UbSite is to employ the composition of k-spaced amino acid pairs surrounding a query site (i.e. any lysine in a query sequence) as input. When trained and tested in the dataset of yeast ubiquitination sites (Radivojac et al, Proteins, 2010, 78: 365-380), a 100-fold cross-validation on a 1∶1 ratio of positive and negative samples revealed that the accuracy and MCC of CKSAAP_UbSite reached 73.40% and 0.4694, respectively. The proposed CKSAAP_UbSite has also been intensively benchmarked to exhibit better performance than some existing predictors, suggesting that it can be served as a useful tool to the community. Currently, CKSAAP_UbSite is freely accessible at http://protein.cau.edu.cn/cksaap_ubsite/. Moreover, we also found that the sequence patterns around ubiquitination sites are not conserved across different species. To ensure a reasonable prediction performance, the application of the current CKSAAP_UbSite should be limited to the proteome of yeast.
format	article
author	Zhen Chen Yong-Zi Chen Xiao-Feng Wang Chuan Wang Ren-Xiang Yan Ziding Zhang
author_facet	Zhen Chen Yong-Zi Chen Xiao-Feng Wang Chuan Wang Ren-Xiang Yan Ziding Zhang
author_sort	Zhen Chen
title	Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs.
title_short	Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs.
title_full	Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs.
title_fullStr	Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs.
title_full_unstemmed	Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs.
title_sort	prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/ff96e5d1d0544d5ca0936e5fe74def59
work_keys_str_mv	AT zhenchen predictionofubiquitinationsitesbyusingthecompositionofkspacedaminoacidpairs AT yongzichen predictionofubiquitinationsitesbyusingthecompositionofkspacedaminoacidpairs AT xiaofengwang predictionofubiquitinationsitesbyusingthecompositionofkspacedaminoacidpairs AT chuanwang predictionofubiquitinationsitesbyusingthecompositionofkspacedaminoacidpairs AT renxiangyan predictionofubiquitinationsitesbyusingthecompositionofkspacedaminoacidpairs AT zidingzhang predictionofubiquitinationsitesbyusingthecompositionofkspacedaminoacidpairs
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Prediction of ubiquitination sites by using the composition of k-spaced amino acid pairs.

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