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. 2011;6(7):e22930.
doi: 10.1371/journal.pone.0022930. Epub 2011 Jul 29.

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

Zhen Chen  1 , Yong-Zi Chen, Xiao-Feng Wang, Chuan Wang, Ren-Xiang Yan, Ziding Zhang
Affiliations

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

Zhen Chen et al. PLoS One. 2011.

Abstract

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. ROC curves of CKSAAP_UbSite and the binary encoding scheme based on balanced ubiquitination and non-ubiquitination sites.
The performance of CKSAAP_UbSite and the binary encoding scheme was assessed through a 100-fold cross-validation strategy.
Figure 2
Figure 2. The composition of the top-25 residue pairs resulting from two feature selection methods.
The composition of each residue pair is represented by a radial vector whose length is proportional to the composition concerned.
Figure 3
Figure 3. Two Two-Sample-Logos of the position-specific residue composition surrounding the ubiquitination sites and non-ubiquitination sites, which were inferred from Radivojac_dataset (A) and Cai_dataset_1 (B), respectively.
These two logos were prepared using the web server http://www.twosamplelogo.org/ and only residues significantly enriched and depleted surrounding ubiquitination sites (t-test, P<0.05) are shown.
Figure 4
Figure 4. Comparison of CKSAAP_UbSite and UbPred based on an independent dataset of 21 proteins.
See this image and copyright information in PMC

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