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Phogly-PseAAC: Prediction of lysine phosphoglycerylation in proteins incorporating with position-specific propensity
Xu, Yan1; Ding, Ya-Xin1; Ding, Jun1; Wu, Ling-Yun2; Deng, Nai-Yang3
2015-08-21
Source PublicationJOURNAL OF THEORETICAL BIOLOGY
ISSN0022-5193
Volume379Pages:10-15
AbstractLarge-scale characterization of post-translational modifications (PTMs), such as posphorylation, acetylation and ubiquitination, has highlighted their importance in the regulation of a myriad of signaling events. However, as another type of PTMs-lysine phosphoglycerylation, the data of phosphoglycerylated sites has just been manually experimented in recent years. Given an uncharacterized protein sequence that contains many lysine residues, which one of them can be phosphoglycerylated and which one not? This is a challenging problem. In view of this, establishing a useful computational method and developing an efficient predictor are highly desired. Here a new predictor named Phogly-PseAAC was developed which incorporated with the position specific amino acid propensity. The feature importance through F-score value has also been ranked. The predictor with the best feature set obtained the accuracy 75.10%, sensitivity 68.87%, specificity 75.57% and MCC 0.2538 in LOO test cross validation with center nearest neighbor algorithm. Meanwhile, a web-server for Phogly-PseAAC is accessible at http://app.aporc.org/Phogly-PseAAC/. For the convenience of most experimental scientists, we have further provided a brief instruction for the web-server, by which users can easily get their desired results without the need to follow the complicated mathematics presented in this paper. It is anticipated that Phogly-PseAAC may become a useful high throughput tool for identifying the lysine phosphoglycerylation sites. (C) 2015 Elsevier Ltd. All rights reserved.
KeywordAmino acid propensity F-score Phosphoglycerylation
DOI10.1016/j.jtbi.2015.04.016
Language英语
Funding ProjectNational Natural Science Foundation of China[11301024] ; National Natural Science Foundation of China[11371365] ; National Natural Science Foundation of China[31201002] ; National Natural Science Foundation of China[11131009]
WOS Research AreaLife Sciences & Biomedicine - Other Topics ; Mathematical & Computational Biology
WOS SubjectBiology ; Mathematical & Computational Biology
WOS IDWOS:000356839700002
PublisherACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
Citation statistics
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/20159
Collection应用数学研究所
Corresponding AuthorXu, Yan
Affiliation1.Univ Sci & Technol Beijing, Dept Informat & Comp Sci, Beijing 100083, Peoples R China
2.Chinese Acad Sci, Inst Appl Math, Acad Math & Syst Sci, Beijing 100190, Peoples R China
3.China Agr Univ, Coll Sci, Beijing 100083, Peoples R China
Recommended Citation
GB/T 7714
Xu, Yan,Ding, Ya-Xin,Ding, Jun,et al. Phogly-PseAAC: Prediction of lysine phosphoglycerylation in proteins incorporating with position-specific propensity[J]. JOURNAL OF THEORETICAL BIOLOGY,2015,379:10-15.
APA Xu, Yan,Ding, Ya-Xin,Ding, Jun,Wu, Ling-Yun,&Deng, Nai-Yang.(2015).Phogly-PseAAC: Prediction of lysine phosphoglycerylation in proteins incorporating with position-specific propensity.JOURNAL OF THEORETICAL BIOLOGY,379,10-15.
MLA Xu, Yan,et al."Phogly-PseAAC: Prediction of lysine phosphoglycerylation in proteins incorporating with position-specific propensity".JOURNAL OF THEORETICAL BIOLOGY 379(2015):10-15.
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