Subcellular Localization Prediction Tools

  • Meinken J, Min XJ. (2012) Computational prediction of protein subcellular locations in eukaryotes: an experience report. Computational Molecular Biology. 2(1): 1-7 (doi: 10.5376/cmb.2012.02.0001).
  • A list of published protein subcellular localization prediction tools
    Tool Name Locations or Protein Features Predicted Organism Categories Publication Reference
    TargetP extracellular, mitochondrial, chloroplast non-plant, plant Emanuelsson, O., Nielsen, H., Brunak, S., & von Heijne, G. (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. Journal of molecular biology, 300(4), 1005-1016.
    TMHMM transmembrane helices any Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of molecular biology, 305(3), 567-580.
    scanProsite (PS-Scan) ER retention signal any de Castro E, Sigrist CJ, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E, Bairoch A, Hulo N. (2006) ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res., 34(Web Server issue), W362-365.
    SecretomeP 2.0 non-classical i.e. not signal peptide triggered protein secretion gram-positive bacteria, gram-negative bacteria, mammal Bendtsen J.D., Jensen,L.J., Blom,N., et al. (2004) Feature based prediction of non-classical and leaderless protein secretion. Protein Eng. Des. Sel., 17, 349-356.
    Phobius signal peptide and transmembrane topology any Käll, L., Krogh, A., & Sonnhammer, E. L. L. (2007) Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server.. Nucleic Acids Res., 35(Web Server issue), W429-432.
    WoLF PSORT > 5 locations fungi, plant, animal Horton, P., Park, K.-J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C. J., & Nakai, K. (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res., 35(Web Server issue), W585-587.
    PRED-LIPO lipoprotein signal peptides gram-positive bacteria Bagos, Pantelis G, Tsirigos, K. D., Liakopoulos, T. D., & Hamodrakas, S. J. (2008) Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model. Journal of proteome research, 7(12), 5082-5093.
    ProLoc-GO > 5 locations human and eukaryotes Huang, W.-L., Tung, C.-W., Ho, S.-W., Hwang, S.-F., & Ho, S.-Y. (2008) ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization. BMC bioinformatics, 9, 80.
    KnowPredsite > 5 locations prokaryotes and eukaryotes Lin, H.-N., Chen, C.-T., Sung, T.-Y., Ho, S.-Y., & Hsu, W.-L. (2009) Protein subcellular localization prediction of eukaryotes using a knowledge-based approach. BMC bioinformatics, 10 Suppl 15, S8.
    MultiLoc2 > 5 locations animal, fungal, plant Blum, T, Briesemeister, S, and Kohlbacher, O (2009) MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BMC Bioinformatics, 10:274.
    PRED-SIGNAL signal peptides archaea Bagos, P G, Tsirigos, K. D., Plessas, S. K., Liakopoulos, T. D., & Hamodrakas, S. J. (2009) Prediction of signal peptides in archaea. Protein engineering, design & selection: PEDS, 22(1), 27-35.
    RSLPred chloroplast, cytoplasm, mitochondria, nucleus oryza sativa only Kaundal, R., & Raghava, G. P. S. (2009) RSLpred: an integrative system for predicting subcellular localization of rice proteins combining compositional and evolutionary information. Proteomics, 9(9), 2324-2342.
    SherLoc2 > 5 locations animal, fungi, plant Briesemeister, S., Blum, T., Brady, S., Lam, Y., Kohlbacher, O., & Shatkay, H. (2009) SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins. Journal of proteome research, 8(11), 5363-5366.
    Cell-PLoc 2.0 > 5 locations eukaryote, human, plant, virus, gram-positive bacteria, gram-negative bacteria Chou, K. and Shen, H. (2010) Cell-PLoc 2.0: an improved package of web-servers for predicting subcellular localization of proteins in various organisms. Natural Science, 2, 1090-1103.
    CoBaltDB > 5 locations prokaryotes Goudenège, D., Avner, S., Lucchetti-Miganeh, C., & Barloy-Hubler, F. (2010) CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources. BMC microbiology, 10, 88.
    PSORTb > 5 locations gram-positive and gram-negative bacteria Yu, N. Y., Wagner, J. R., Laird, M. R., Melli, G., Rey, S., Lo, R., ... Brinkman, F. S. L. (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics (Oxford, England), 26(13), 1608-1615.
    SCLPred cytoplasm, mitochondrion, nucleus, secretory, chloroplast animals, plants, fungi Mooney, C., Wang, Y.-H., & Pollastri, G. (2011) SCLpred: protein subcellular localization prediction by N-to-1 neural networks. Bioinformatics (Oxford, England), 27(20), 2812-2819.
    SignalP 4.0 signal peptide eukaryotic, gram-positive bacteria, gram-negative bacteria Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H. (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature methods, 8(10), 785-786.
    SlocX > 5 locations aribdopsis thaliana only Ryngajllo, M., Childs, L., Lohse, M., Giorgi, F. M., Lude, A., Selbig, J., & Usadel, B. (2011) SLocX: Predicting Subcellular Localization of Arabidopsis Proteins Leveraging Gene Expression Data. Frontiers in plant science, 2, 43.
    APSLAP > 5 locations apoptosis Saravanan, V., & Lakshmi, P. T. V. (2013) APSLAP: An Adaptive Boosting Technique for Predicting Subcellular Localization of Apoptosis Protein. Acta biotheoretica, .
    Iloc Animal > 5 locations animal Lin, W.-Z., Fang, J.-A., Xiao, X., & Chou, K.-C. (2013) iLoc-Animal: a multi-label learning classifier for predicting subcellular localization of animal proteins. Molecular bioSystems, 9(4), 634-644.