iSNO-PseAAC

iSNO-PseAAC: predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition. Posttranslational modifications (PTMs) of proteins are responsible for sensing and transducing signals to regulate various cellular functions and signaling events. S-nitrosylation (SNO) is one of the most important and universal PTMs. With the avalanche of protein sequences generated in the post-genomic age, it is highly desired to develop computational methods for timely identifying the exact SNO sites in proteins because this kind of information is very useful for both basic research and drug development. Here, a new predictor, called iSNO-PseAAC, was developed for identifying the SNO sites in proteins by incorporating the position-specific amino acid propensity (PSAAP) into the general form of pseudo amino acid composition (PseAAC). The predictor was implemented using the conditional random field (CRF) algorithm. As a demonstration, a benchmark dataset was constructed that contains 731 SNO sites and 810 non-SNO sites. To reduce the homology bias, none of these sites were derived from the proteins that had [Formula: see text] pairwise sequence identity to any other. It was observed that the overall cross-validation success rate achieved by iSNO-PseAAC in identifying nitrosylated proteins on an independent dataset was over 90%, indicating that the new predictor is quite promising. Furthermore, a user-friendly web-server for iSNO-PseAAC was established at http://app.aporc.org/iSNO-PseAAC/, by which users can easily obtain the desired results without the need to follow the mathematical equations involved during the process of developing the prediction method. It is anticipated that iSNO-PseAAC may become a useful high throughput tool for identifying the SNO sites, or at the very least play a complementary role to the existing methods in this area.


References in zbMATH (referenced in 39 articles )

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  1. Chen, Guodong; Cao, Man; Yu, Jialin; Guo, Xinyun; Shi, Shaoping: Prediction and functional analysis of prokaryote lysine acetylation site by incorporating six types of features into Chou’s general PseAAC (2019)
  2. 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)
  3. Ning, Qiao; Ma, Zhiqiang; Zhao, Xiaowei: Dforml(KNN)-PseAAC: detecting formylation sites from protein sequences using K-nearest neighbor algorithm via Chou’s 5-step rule and pseudo components (2019)
  4. 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)
  5. Tian, Baoguang; Wu, Xue; Chen, Cheng; Qiu, Wenying; Ma, Qin; Yu, Bin: Predicting protein-protein interactions by fusing various Chou’s pseudo components and using wavelet denoising approach (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. 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)
  8. 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)
  9. 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)
  10. 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)
  11. Qiu, Wenying; Li, Shan; Cui, Xiaowen; Yu, Zhaomin; Wang, Minghui; Du, Junwei; Peng, Yanjun; Yu, Bin: Predicting protein submitochondrial locations by incorporating the pseudo-position specific scoring matrix into the general Chou’s pseudo-amino acid composition (2018)
  12. Sabooh, M. Fazli; Iqbal, Nadeem; Khan, Mukhtaj; Khan, Muslim; Maqbool, H. F.: Identifying 5-methylcytosine sites in RNA sequence using composite encoding feature into Chou’s PseKNC (2018)
  13. Tarafder, Sumit; Toukir Ahmed, Md.; Iqbal, Sumaiya; Tamjidul Hoque, Md; Sohel Rahman, M.: RBSURFpred: modeling protein accessible surface area in real and binary space using regularized and optimized regression (2018)
  14. 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)
  15. Jia, Jianhua; Liu, Zi; Xiao, Xuan; Liu, Bingxiang; Chou, Kuo-Chen: pSuc-Lys: predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach (2016)
  16. Ju, Zhe; Cao, Jun-Zhe; Gu, Hong: iLM-2L: a two-level predictor for identifying protein lysine methylation sites and their methylation degrees by incorporating K-gap amino acid pairs into Chou’s general PseAAC (2015)
  17. Khan, Zaheer Ullah; Hayat, Maqsood; Khan, Muazzam Ali: Discrimination of acidic and alkaline enzyme using Chou’s pseudo amino acid composition in conjunction with probabilistic neural network model (2015)
  18. Kumar, Ravindra; Srivastava, Abhishikha; Kumari, Bandana; Kumar, Manish: Prediction of (\beta)-lactamase and its class by Chou’s pseudo-amino acid composition and support vector machine (2015)
  19. Li, Chun; Yang, Yan; Fei, Wenchao; He, Ping-an; Yu, Xiaoqing; Zhang, Defu; Yi, Shumin; Li, Xuepeng; Zhu, Jin; Wang, Changzhong; Wang, Zhifu: Prediction of success for polymerase chain reactions using the Markov maximal order model and support vector machine (2015)
  20. Li, Xiong; Liao, Bo; Chen, Haowen: A new technique for generating pathogenic barcodes in breast cancer susceptibility analysis (2015)

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