Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs
文献类型：期刊论文
| 作者 | Hasan, Md. Mehedi1; Zhou, Yuan1; Lu, Xiaotian1; Li, Jinyan2; Song, Jiangning3,4,5,6; Zhang, Ziding1 |
| 刊名 | PLOS ONE
 |
| 出版日期 | 2015-06-16 |
| 卷号 | 10期号:6 |
| 英文摘要 | Prokaryotic proteins are regulated by pupylation, a type of post-translational modification that contributes to cellular function in bacterial organisms. In pupylation process, the prokaryotic ubiquitin-like protein (Pup) tagging is functionally analogous to ubiquitination in order to tag target proteins for proteasomal degradation. To date, several experimental methods have been developed to identify pupylated proteins and their pupylation sites, but these experimental methods are generally laborious and costly. Therefore, computational methods that can accurately predict potential pupylation sites based on protein sequence information are highly desirable. In this paper, a novel predictor termed as pbPUP has been developed for accurate prediction of pupylation sites. In particular, a sophisticated sequence encoding scheme [i.e. the profile-based composition of k-spaced amino acid pairs (pbCKSAAP)] is used to represent the sequence patterns and evolutionary information of the sequence fragments surrounding pupylation sites. Then, a Support Vector Machine (SVM) classifier is trained using the pbCKSAAP encoding scheme. The final pbPUP predictor achieves an AUC value of 0.849 in 10-fold cross-validation tests and outperforms other existing predictors on a comprehensive independent test dataset. The proposed method is anticipated to be a helpful computational resource for the prediction of pupylation sites. The web server and curated datasets in this study are freely available at http://protein.cau.edu.cn/pbPUP/. |
| WOS标题词 | Science & Technology |
| 类目[WOS] | Multidisciplinary Sciences |
| 研究领域[WOS] | Science & Technology - Other Topics |
| 关键词[WOS] | UBIQUITIN-LIKE PROTEIN ; MYCOBACTERIUM-TUBERCULOSIS ; PROTEASOMAL DEGRADATION ; PUP ; PREDICTION ; PATHWAY ; SIGNAL ; METHYLATION ; CASCLEAVE ; CASPASE |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000356542300028 |
| 源URL | [http://124.16.173.210/handle/834782/1494]  |
| 专题 | 天津工业生物技术研究所_结构生物信息学和整合系统生物学实验室 宋江宁_期刊论文 |
| 作者单位 | 1.China Agr Univ, Coll Biol Sci, State Key Lab Agrobiotechnol, Beijing 100193, Peoples R China 2.Univ Technol Sydney, Adv Analyt Inst & Ctr Hlth Technol, Sydney, NSW 2007, Australia 3.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Natl Engn Lab Ind Enzymes, Tianjin 300308, Peoples R China 4.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Key Lab Syst Microbial Biotechnol, Tianjin 300308, Peoples R China 5.Monash Univ, Fac Med, Monash Bioinformat Platform, Melbourne, Vic 3800, Australia 6.Monash Univ, Fac Med, Dept Biochem & Mol Biol, Melbourne, Vic 3800, Australia |
| 推荐引用方式 GB/T 7714 | Hasan, Md. Mehedi,Zhou, Yuan,Lu, Xiaotian,et al. Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs[J]. PLOS ONE,2015,10(6). |
| APA | Hasan, Md. Mehedi,Zhou, Yuan,Lu, Xiaotian,Li, Jinyan,Song, Jiangning,&Zhang, Ziding.(2015).Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs.PLOS ONE,10(6). |
| MLA | Hasan, Md. Mehedi,et al."Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs".PLOS ONE 10.6(2015). |
入库方式： OAI收割
来源：天津工业生物技术研究所
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