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

References in zbMATH (referenced in 16 articles )

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  1. Adilina, Sheikh; Farid, Dewan Md; Shatabda, Swakkhar: Effective DNA binding protein prediction by using key features via Chou’s general PseAAC (2019)
  2. Hussain, Waqar; Khan, Yaser Daanial; Rasool, Nouman; Khan, Sher Afzal; Chou, Kuo-Chen: SPrenylC-PseAAC: a sequence-based model developed via Chou’s 5-steps rule and general PseAAC for identifying S-prenylation sites in proteins (2019)
  3. Jia, Jianhua; Li, Xiaoyan; Qiu, Wangren; Xiao, Xuan; Chou, Kuo-Chen: iPPI-PseAAC(CGR): identify protein-protein interactions by incorporating chaos game representation into PseAAC (2019)
  4. Qing, Yang; Cangzhi, Jia; Taoying, Li: Prediction of aptamer-protein interacting pairs based on sparse autoencoder feature extraction and an ensemble classifier (2019)
  5. Tahir, Muhammad; Tayara, Hilal; Chong, Kil To: iRNA-PseKNC(2methyl): identify RNA 2’-O-methylation sites by convolution neural network and Chou’s pseudo components (2019)
  6. Wang, Lidong; Zhang, Ruijun; Mu, Yashuang: Fu-SulfPred: identification of protein S-sulfenylation sites by fusing forests via Chou’s general PseAAC (2019)
  7. Zhao, Xiaowei; Zhang, Ye; Ning, Qiao; Zhang, Hongrui; Ji, Jinchao; Yin, Minghao: Identifying N(^6)-methyladenosine sites using extreme gradient boosting system optimized by particle swarm optimizer (2019)
  8. Akbar, Shahid; Hayat, Maqsood: iMethyl-STTNC: identification of N(^6)-methyladenosine sites by extending the idea of SAAC into Chou’s PseAAC to formulate RNA sequences (2018)
  9. Arif, Muhammad; Hayat, Maqsood; Jan, Zahoor: IMem-2LSAAC: a two-level model for discrimination of membrane proteins and their types by extending the notion of SAAC into Chou’s pseudo amino acid composition (2018)
  10. Cheng, Xiang; Xiao, Xuan; Chou, Kuo-Chen: pLoc_bal-mGneg: predict subcellular localization of Gram-negative bacterial proteins by quasi-balancing training dataset and general PseAAC (2018)
  11. Ju, Zhe; Wang, Shi-Yun: Prediction of S-sulfenylation sites using mRMR feature selection and fuzzy support vector machine algorithm (2018)
  12. Mei, Juan; Fu, Yi; Zhao, Ji: Analysis and prediction of ion channel inhibitors by using feature selection and Chou’s general pseudo amino acid composition (2018)
  13. Goede, Simon L.; de Galan, Bastiaan E.; Leow, Melvin Khee Shing: Personalized glucose-insulin model based on signal analysis (2017)
  14. Khan, Muslim; Hayat, Maqsood; Khan, Sher Afzal; Ahmad, Saeed; Iqbal, Nadeem: Bi-PSSM: position specific scoring matrix based intelligent computational model for identification of mycobacterial membrane proteins (2017)
  15. Zhai, Jing-Xuan; Cao, Tian-Jie; An, Ji-Yong; Bian, Yong-Tao: Highly accurate prediction of protein self-interactions by incorporating the average block and PSSM information into the general PseAAC (2017)
  16. Yang, Lei; Wang, Shiyuan; Zhou, Meng; Chen, Xiaowen; Zuo, Yongchun; Lv, Yingli: Characterization of BioPlex network by topological properties (2016)