iLoc-Hum

iLoc-Hum: using the accumulation-label scale to predict subcellular locations of human proteins with both single and multiple sites. Although numerous efforts have been made for predicting the subcellular locations of proteins based on their sequence information, it still remains as a challenging problem, particularly when query proteins may have the multiplex character, i.e., they simultaneously exist, or move between, two or more different subcellular location sites. Most of the existing methods were established on the assumption: a protein has one, and only one, subcellular location. Actually, recent evidence has indicated an increasing number of human proteins having multiple subcellular locations. This kind of multiplex proteins should not be ignored because they may bear some special biological functions worthy of our attention. Based on the accumulation-label scale, a new predictor, called iLoc-Hum, was developed for identifying the subcellular localization of human proteins with both single and multiple location sites. As a demonstration, the jackknife cross-validation was performed with iLoc-Hum on a benchmark dataset of human proteins that covers the following 14 location sites: centrosome, cytoplasm, cytoskeleton, endoplasmic reticulum, endosome, extracellular, Golgi apparatus, lysosome, microsome, mitochondrion, nucleus, peroxisome, plasma membrane, and synapse, where some proteins belong to two, three or four locations but none has 25% or higher pairwise sequence identity to any other in the same subset. For such a complicated and stringent system, the overall success rate achieved by iLoc-Hum was 76%, which is remarkably higher than that by any of the existing predictors that also have the capacity to deal with this kind of system. Further comparisons were also made via two independent datasets; all indicated that the success rates by iLoc-Hum were even more significantly higher than its counterparts. As a user-friendly web-server, iLoc-Hum is freely accessible to the public at or . For the convenience of most experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results by choosing either a straightforward submission or a batch submission, without the need to follow the complicated mathematical equations involved.


References in zbMATH (referenced in 26 articles )

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  1. 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)
  2. Shen, Yinan; Tang, Jijun; Guo, Fei: Identification of protein subcellular localization via integrating evolutionary and physicochemical information into Chou’s general PseAAC (2019)
  3. 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)
  4. 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)
  5. 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)
  6. Sankari, E. Siva; Manimegalai, D.: Predicting membrane protein types by incorporating a novel feature set into Chou’s general PseAAC (2018)
  7. 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)
  8. Zhang, Shengli; Duan, Xin: Prediction of protein subcellular localization with oversampling approach and Chou’s general PseAAC (2018)
  9. 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)
  10. Jiao, Ya-Sen; Du, Pu-Feng: Predicting Golgi-resident protein types using pseudo amino acid compositions: approaches with positional specific physicochemical properties (2016)
  11. Jiao, Ya-Sen; Du, Pu-Feng: Prediction of Golgi-resident protein types using general form of Chou’s pseudo-amino acid compositions: approaches with minimal redundancy maximal relevance feature selection (2016)
  12. Muthu Krishnan, S.: Classify vertebrate hemoglobin proteins by incorporating the evolutionary information into the general PseAAC with the hybrid approach (2016)
  13. Ali, Farman; Hayat, Maqsood: Classification of membrane protein types using voting feature interval in combination with Chou’s pseudo amino acid composition (2015)
  14. 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)
  15. Wan, Shibiao; Mak, Man-Wai; Kung, Sun-Yuan: mLASSO-Hum: a LASSO-based interpretable human-protein subcellular localization predictor (2015)
  16. Fan, Guo-Liang; Li, Qian-Zhong: Discriminating bioluminescent proteins by incorporating average chemical shift and evolutionary information into the general form of Chou’s pseudo amino acid composition (2013)
  17. Feng, Peng-Mian; Ding, Hui; Chen, Wei; Lin, Hao: Naïve Bayes classifier with feature selection to identify phage virion proteins (2013)
  18. Huang, Chao; Yuan, Jing-Qi: Predicting protein subchloroplast locations with both single and multiple sites via three different modes of Chou’s pseudo amino acid compositions (2013)
  19. Pan, Lu-Lu; Wang, Yu; Hu, Jian-Hui; Ding, Zhao-Tang; Li, Chen: Analysis of codon use features of stearoyl-acyl carrier protein desaturase gene in \textitCamelliasinensis (2013)
  20. Zhou, Xuan; Li, Zhanchao; Dai, Zong; Zou, Xiaoyong: Predicting promoters by pseudo-trinucleotide compositions based on discrete wavelets transform (2013)

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