iLoc-Plant: a multi-label classifier for predicting the subcellular localization of plant proteins with both single and multiple sites. Predicting protein subcellular localization is a challenging problem, particularly when query proteins may simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing methods can only be used to deal with the single-location proteins. Actually, multiple-location proteins should not be ignored because they usually bear some special functions worthy of our notice. By introducing the “multi-labeled learning” approach, a new predictor, called iLoc-Plant, has been developed that can be used to deal with the systems containing both single- and multiple-location plant proteins. As a demonstration, the jackknife cross-validation was performed with iLoc-Plant on a benchmark dataset of plant proteins classified into the following 12 location sites: (1) cell membrane, (2) cell wall, (3) chloroplast, (4) cytoplasm, (5) endoplasmic reticulum, (6) extracellular, (7) Golgi apparatus, (8) mitochondrion, (9) nucleus, (10) peroxisome, (11) plastid, and (12) vacuole, where some proteins belong to two or three locations but none has ≥25% pairwise sequence identity to any other in a same subset. The overall success rate thus obtained by iLoc-Plant was 71%, which is remarkably higher than those achieved by any existing predictors that also have the capacity to deal with such a stringent and complicated plant protein system. As a user-friendly web-server, iLoc-Plant is freely accessible to the public at the web-site or Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematic equations presented in this paper for its integrity. It is anticipated that iLoc-Plant may become a useful bioinformatics tool for Molecular Cell Biology, Proteomics, Systems Biology, and Drug Development.

References in zbMATH (referenced in 18 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. Zhang, Shengli; Duan, Xin: Prediction of protein subcellular localization with oversampling approach and Chou’s general PseAAC (2018)
  4. Jiao, Xiong; Ranganathan, Shoba: Prediction of interface residue based on the features of residue interaction network (2017)
  5. 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)
  6. Jiao, Ya-Sen; Du, Pu-Feng: Predicting Golgi-resident protein types using pseudo amino acid compositions: approaches with positional specific physicochemical properties (2016)
  7. Golzari, Fahimeh; Jalili, Saeed: VR-BFDT: a variance reduction based binary fuzzy decision tree induction method for protein function prediction (2015)
  8. Li, Xiaomei; Wu, Xindong; Wu, Gongqing: Robust feature generation for protein subchloroplast location prediction with a weighted GO transfer model (2014)
  9. Lyons, James; Biswas, Neela; Sharma, Alok; Dehzangi, Abdollah; Paliwal, Kuldip K.: Protein fold recognition by alignment of amino acid residues using kernelized dynamic time warping (2014)
  10. Tahir, Muhammad; Khan, Asifullah; Kaya, Hüseyin: Protein subcellular localization in human and hamster cell lines: employing local ternary patterns of fluorescence microscopy images (2014)
  11. Yang, Lei; Lv, Yingli; Li, Tao; Zuo, Yongchun; Jiang, Wei: Human proteins characterization with subcellular localizations (2014)
  12. 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)
  13. Fan, Guo-Liang; Li, Qian-Zhong: Predicting mycobacterial proteins subcellular locations by incorporating pseudo-average chemical shift into the general form of Chou’s pseudo amino acid composition (2012)
  14. Jahandideh, Samad; Mahdavi, Abbas: RFCRYS: sequence-based protein crystallization propensity prediction by means of random forest (2012)
  15. Jahandideh, Samad; Srinivasasainagendra, Vinodh; Zhi, Degui: Comprehensive comparative analysis and identification of RNA-binding protein domains: multi-class classification and feature selection (2012)
  16. Li, Tao; Li, Qian-Zhong: Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure (2012)
  17. Mei, Suyu: Predicting plant protein subcellular multi-localization by Chou’s PseAAC formulation based multi-label homolog knowledge transfer learning (2012)
  18. Mishra, Pooja; Nath Pandey, Paras: Elman RNN based classification of proteins sequences on account of their mutual information (2012)