iPhos-PseEn: Identifying phosphorylation sites in proteins by fusing different pseudo components into an ensemble classifier

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Abstract

Protein phosphorylation is a posttranslational modification (PTM or PTLM), where a phosphoryl group is added to the residue(s) of a protein molecule. The most commonly phosphorylated amino acids occur at serine (S), threonine (T), and tyrosine (Y). Protein phosphorylation plays a significant role in a wide range of cellular processes; meanwhile its dysregulation is also involved with many diseases. Therefore, from the angles of both basic research and drug development, we are facing a challenging problem: For an uncharacterized protein sequence containing many residues of S, T, or Y, which ones can be phosphorylated, and which ones cannot? To address this problem, we have developed a predictor called iPhos-PseEn by fusing four different pseudo component approaches (amino acids' disorder scores, nearest neighbor scores, occurrence frequencies, and position weights) into an ensemble classifier via a voting system. Rigorous cross-validations indicated that the proposed predictor remarkably outperformed its existing counterparts. For the convenience of most experimental scientists, a user-friendly web-server for iPhos- PseEn has been established at http://www.jci-bioinfo.cn/iPhos-PseEn, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.

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Qiu, W. R., Xiao, X., Xu, Z. C., & Chou, K. C. (2016). iPhos-PseEn: Identifying phosphorylation sites in proteins by fusing different pseudo components into an ensemble classifier. Oncotarget, 7(32), 51270–51283. https://doi.org/10.18632/oncotarget.9987

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