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PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization

Nakai, Kenta, Horton, Paul·1999·Trends in Biochemical Sciences

DOI 10.1016/s0968-0004(98)01336-x

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Horton, 1996, Intelligent Systems for Molecular Biology, 4, 109
Horton, 1997, Intelligent Systems for Molecular Biology, 5, 147
Nakai, K.(1996) in Genome Informatics 1996 (Vol. 7) (Akutsu, T. et al.., eds), pp. 72-81, Universal Academy Press
Bairoch, 1997, Nucleic Acids Res., 25, 217, 10.1093/nar/25.1.217 · DOI

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Cerritelli, S. M., Frolova, E. G., Feng, C., Grinberg, A., Love, P. E., & Crouch, R. J. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00088-1 · Cited by 358
NucPred—Predicting nuclear localization of proteins
Brameier, M., Krings, A., & MacCallum, R. M. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm066 · Cited by 359
&cestflwr; The Hsp90 family of proteins in Arabidopsis thaliana
Krishna, P., & Gloor, G. B. (2001) · Cell Stress and Chaperones · doi:10.1379/1466-1268(2001)006 · Cited by 360
The Cytochrome P450 Enzyme CYP96A15 Is the Midchain Alkane Hydroxylase Responsible for Formation of Secondary Alcohols and Ketones in Stem Cuticular Wax of Arabidopsis
Greer, S. P., Wen, M., Bird, D. A., et al. (2007) · PLANT PHYSIOLOGY · doi:10.1104/pp.107.107300 · Cited by 357
“Vol. 145, 2007 661 SignalP 3.0 with defaults; Bendtsen et al., 2004; Emanuelsson et al., 2007) with secretory/ER targeting (TargetP 1.1 5 0.970; WoLF PSORT 5 5.0 with defaults; Nakai and Horton, 1999; Bendtsen et al., 2004; Emanuelsson et al., 2007).”
BackgroundInfluential
Export of mitochondrial AIF in response to proapoptotic stimuli depends on processing at the intermembrane space
Otera, H., Ohsakaya, S., Nagaura, Z.-I., Ishihara, N., & Mihara, K. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600614 · Cited by 354
“The PSORT II program (Nakai and Horton, 1999) predicts that the 17-amino-acid region between positions 67 and 83 of the AIF precursor functions as the TMS.”
Method
Proteomics of the Chloroplast: Systematic Identification and Targeting Analysis of Lumenal and Peripheral Thylakoid Proteins
Peltier, J., Friso, G., Kalume, D. E., Roepstorff, P., Nilsson, F., Adamska, I., & van Wijka, K. J. (2000) · The Plant Cell · doi:10.1105/tpc.12.3.319 · Cited by 356
“The presequences of these nuclear-encoded chloroplast proteins share common features, which can be used to predict localization with moderate confidence (Emanuelsson et al., 1999; Nakai and Horton, 1999).”
BackgroundMethodInfluential
Use of a Whole Genome Approach To Identify Vaccine Molecules Affording Protection against Streptococcus pneumoniae Infection
Wizemann, T. M., Heinrichs, J. H., Adamou, J. E., Erwin, A. L., KUNSCH, C. A., Choi, G. H., Barash, S. C., Rosen, C. A., Masure, H. R., TUOMANEN, E. I., et al. (2001) · Infection and Immunity · doi:10.1128/iai.69.3.1593-1598.2001 · Cited by 351
“The products of 108 of these ORFs, comprising 97 unique genes or their subfragments, were successfully expressed and purified for evaluation as vaccine a Amino acid sequences are represented by single-letter designations; “X” indicates any amino acid; any amino acid in parentheses may occupy the position indicated. b…”
Method
Cell-PLoc 2.0: an improved package of web-servers for predicting subcellular localization of proteins in various organisms
Chou, K., & Shen, H. (2010) · Natural Science · doi:10.4236/ns.2010.210136 · Cited by 348
“, [4-59].”
Sequence Identification and Characterization of Human Carnosinase and a Closely Related Non-specific Dipeptidase
Teufel, M., Saudek, V., Ledig, J.-P., Bernhardt, A., Boularand, S., Carreau, A., Cairns, N. J., Carter, C. J., Cowley, D. J., Duverger, D., et al. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m209764200 · Cited by 346
Cloning and Sequence Analysis of a Highly PolymorphicCryptosporidium parvumGene Encoding a 60-Kilodalton Glycoprotein and Characterization of Its 15- and 45-Kilodalton Zoite Surface Antigen Products
Strong, W. B., Gut, J., & Nelson, R. G. (2000) · Infection and Immunity · doi:10.1128/iai.68.7.4117-4134.2000 · Cited by 343
“The amino terminus of the sequence contained a string of hydrophobic and hydroxylic amino acid residues that were predicted by the PSORT II program (57) to constitute an N-terminal signal sequence with a signal peptidase cleavage site between amino acids Ser19 and Ala20; similarly, the hydrophobic C terminus of the se…”
Background
BaCelLo: a balanced subcellular localization predictor
Pierleoni, A., Martelli, P. L., Fariselli, P., & Casadio, R. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl222 · Cited by 338
“…others discriminate among four classes in animals and ﬁve classes in plants and are Loctree, SubLoc, ESLpred and LOCSVMpsi. pTARGET and Psort II (Nakai and Horton, 1999) discriminate more classes than BaCelLo does, however we did not consider these classes since very few redundant examples are…”
Background
A Proteomics Dissection of Arabidopsis thaliana Vacuoles Isolated from Cell Culture
Jaquinod, M., Villiers, F., Kieffer‐Jaquinod, S., Hugouvieux, V., Bruley, C., Garin, J., & Bourguignon, J. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m600250-mcp200 · Cited by 346
“Complementary information was obtained using the Psort II prediction program (54).”
Method
iLoc-Hum: using the accumulation-label scale to predict subcellular locations of human proteins with both single and multiple sites
Chou, K., Wu, Z., & Xiao, X. (2011) · Molecular BioSystems · doi:10.1039/c1mb05420a · Cited by 334
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, T., Itoh, T., Suzuki, Y., O’Donovan, C., Fukuchi, S., Koyanagi, K. O., Barrero, R. A., Tamura, T., Yamaguchi‐Kabata, Y., Tanino, M., et al. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020162 · Cited by 331
“Subcellular localization targeting signals and transmembrane helices of 40,352 H-Inv proteins were predicted using the PSORT II (Nakai and Horton 1999), TargetP (Emanuelsson et al.”
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition
Höglund, A., Dönnes, P., Blum, T., Adolph, H., & Kohlbacher, O. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl002 · Cited by 325
“The most comprehensive prediction system reported so far, PSORT, is based on a collection of expert if-then rules originating from experimental and computational observations (Nakai & Kanehisa, 1992; Nakai & Horton, 1999).”
BackgroundResultInfluential
Protein sorting signals and prediction of subcellular localization
Nakai, K. (2000) · Advances in protein chemistry · doi:10.1016/s0065-3233(00)54009-1 · Cited by 320
Self-citation
The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions
Leahy, S. C., Kelly, W. J., Altermann, E., Ronimus, R. S., Yeoman, C. J., Pacheco, D. M., Li, D., Kong, Z., McTavish, S. M., Sang, C., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008926 · Cited by 318
“) was used for the prediction of transmembrane domains and PSORT”
Method
Euk-mPLoc: A Fusion Classifier for Large-Scale Eukaryotic Protein Subcellular Location Prediction by Incorporating Multiple Sites
Chou, K., & Shen, H. (2007) · Journal of Proteome Research · doi:10.1021/pr060635i · Cited by 319
“The predictor obtained through the above modified procedures is called Euk-mPLoc (i) that Figure 1. Schematic illustration to show the 22 subcellular locations of eukaryotic proteins: (1) acrosome, (2) cell wall, (3) centriole, (4) chloroplast, (5) cyanelle, ( 6 ) cytoplasm, (7) cytoskeleton, (8) endoplasmic reticulum…”
Prediction of Human Protein Function from Post-translational Modifications and Localization Features
Jensen, L. J., Gupta, R., Blom, N., Devos, D. P., Tamames, J., Keşmir, C., Nielsen, H., Stærfeldt, H., Rapacki, K., Workman, C. T., et al. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00379-0 · Cited by 317
“As several predictive methods for PTMs have been constructed (R.G., S.B., unpublished results), 10–13 a function prediction method based on such attributes can be applied to all proteins where the sequence is known.”
Method
Germline loss-of-function mutations in LZTR1 predispose to an inherited disorder of multiple schwannomas
Piotrowski, A., Xie, J., Liu, Y. F., Poplawski, A. B., Gomes, A., Madanecki, P., Fu, C., Crowley, M. R., Crossman, D. K., Armstrong, L., et al. (2013) · Nature Genetics · doi:10.1038/ng.2855 · Cited by 326
Mineralized tissue and vertebrate evolution: The secretory calcium-binding phosphoprotein gene cluster
Kawasaki, K., & Weiss, K. M. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0638023100 · Cited by 314
Getting to the roots of parasitism by nematodes
Davis, E. (2004) · Trends in Parasitology · doi:10.1016/j.pt.2004.01.005 · Cited by 317
Adenosine Kinase: Exploitation for Therapeutic Gain
Boison, D. (2013) · Pharmacological Reviews · doi:10.1124/pr.112.006361 · Cited by 320
“Founded on algorithms that predict subcellular localization based on sequence similarities, it was initially speculated that both isoforms of ADK are located in the cytoplasm (Nakai and Horton, 1999; Sakowicz et al., 2001).”
Background
ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST
Bhasin, M., & Raghava, G. P. S. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh350 · Cited by 310
“Thepredictionaccuracyforeukaryoticproteinswas (9).”
Functional Analysis of a Human Homologue of the Drosophila Actin Binding Protein Anillin Suggests a Role in Cytokinesis
Oegema, K., Savoian, M. S., Mitchison, T. J., & Field, C. M. (2000) · The Journal of Cell Biology · doi:10.1083/jcb.150.3.539 · Cited by 309
“The locations of potential nuclear localization sequences, identified using the program PSORT II ( Nakai and Horton, 1999 ), are indicated with black triangles (human, amino acids 64, 66, 195, 786, 896, and 1,021; Drosophila, amino acids 996 and 1,105).”
Method
Molecular cloning and expression analyses of mouse βklotho, which encodes a novel Klotho family protein
Ito, S., Kinoshita, S., Shiraishi, N., Nakagawa, S., Sekine, S., Fujimori, T., & Nabeshima, Y. (2000) · Mechanisms of Development · doi:10.1016/s0925-4773(00)00439-1 · Cited by 312
“Using the protein sorting prediction program (PSORTII; Nakai and Horton, 1999), we determined that like KL, bKL possesses a putative signal sequence at its Nterminus and a membrane-spanning region with short hydrophilic tail at the C-terminus.”
Mutations in PMR5 result in powdery mildew resistance and altered cell wall composition
Vogel, J. P., Raab, T. K., Somerville, C. R., & Somerville, S. C. (2004) · The Plant Journal · doi:10.1111/j.1365-313x.2004.02264.x · Cited by 300
“The first 22 aa of PMR5 are predicted to serve as a non-cleavable signal sequence that targets the protein to the endoplasmic reticulum (Target P: Olof et al., 2000; PSORT: Nakai and Horton, 1999; ProtFun 1.1: Jensen et al., 2002).”
BackgroundInfluential
Intracellular substrate cleavage: a novel dimension in the biochemistry, biology and pathology of matrix metalloproteinases
Cauwe, B., & Opdenakker, G. (2010) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238.2010.501783 · Cited by 298
“Using the bioinformatics software PSORT (Nakai and Horton, 1999), they detected a putative NLS (PKWRKTH) at position 107 to 113 in the catalytical domain, which was well conserved between the human, mouse and rat sequences of MMP-3.”
Method
Acetyl-CoA Synthetase 2, a Mitochondrial Matrix Enzyme Involved in the Oxidation of Acetate
Fujino, T., Kondo, J., Ishikawa, M., Morikawa, K., & Yamamoto, T. T. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m008782200 · Cited by 298
Protein Transport into Chloroplasts
Li, H., & Chiu, C.-C. (2010) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-042809-112222 · Cited by 296
Mimicking Cellular Sorting Improves Prediction of Subcellular Localization
Nair, R. P., & Rost, B. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.02.025 · Cited by 290
“Comparison with other methods using additional test sets Other methods tested on new data set We compared our method to the following publicly available methods: TargetP, 33 SubLoc, 67 NNPSL, 40 and PSORT II.”
Method
A Multi-Label Classifier for Predicting the Subcellular Localization of Gram-Negative Bacterial Proteins with Both Single and Multiple Sites
Xiao, X., Wu, Z.-C., & Chou, K. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020592 · Cited by 284
“They are called ‘‘PSORT’’ [1,3,4], ‘‘PSORT-B’’ [5], and PSORTb v.”
Identification of a Protein from Rust Fungi Transferred from Haustoria into Infected Plant Cells
Kemen, E. M., Kemen, A. C., Rafiqi, M., Hempel, U., Mendgen, K. W., Hahn, M., & Voegele, R. T. (2005) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-18-1130 · Cited by 296
“AUTHOR-RECOMMENDED INTERNET RESOURCES PSORTII: psort.ims.u-tokyo.ac.jp/form2.html SignalP V2.”
The Parasitome of the Phytonematode Heterodera glycines
Gao, B., Allen, R., Maier, T. R., Davis, E., Baum, T. J., & HUSSEY, R. S. (2003) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi.2003.16.8.720 · Cited by 282
“Transmembrane regions and subcellular localization sites of the deduced proteins were predicted by TMHMM (Krogh et al. 2001) and PSORT II (Nakai and Horton 1999), respectively.”
Method
Diverse Targets of Phytoplasma Effectors: From Plant Development to Defense Against Insects
Sugio, A., MacLean, A. M., Kingdom, H. N., Grieve, V. M., Manimekalai, R., & Hogenhout, S. A. (2011) · Annual Review of Phytopathology · doi:10.1146/annurev-phyto-072910-095323 · Cited by 290
“PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization.”
Background
Transgene and Transposon Silencing in Chlamydomonas reinhardtii by a DEAH-Box RNA Helicase
Wu‐Scharf, D., Jeong, B., Zhang, C. H., & Cerutti, H. D. (2000) · Science · doi:10.1126/science.290.5494.1159 · Cited by 280
Quantitative Proteomic Comparison of Rat Mitochondria from Muscle, Heart, and Liver
Forner, F., Foster, L. J., Campanaro, S., Valle, G., & Mann, M. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500298-mcp200 · Cited by 280
“Mitopred or PSORT II (39), such as acid phosphatase 6 (with”
Peroxisome targeting signal 1: Is it really a simple tripeptide?
Brocard, C., & Hartig, A. (2006) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2006.08.022 · Cited by 278
“In Table 1 the PTS1-predictor is compared with the established PSORTII [69].”
Method

Authors: Nakai, K., & Horton, P.
Affiliations: The University of Osaka (JP)
Corresponding author: Nakai, Kenta
ORCID: Nakai, Kenta
Horton, Paul
Venue: Trends in Biochemical Sciences
Publisher: Elsevier BV
Published: 1999-01
Volume: 24
Issue: 1
Pages: 34-35
ISSN: 0968-0004 (ISSN-L)
DOI: 10.1016/s0968-0004(98)01336-x
OpenAlex: W2006211612
Cited by: 2,181
References: 13
Citations by year: 2026: 25 · 2025: 26 · 2024: 43 · 2023: 33 · 2022: 23 · 2021: 31 · 2020: 36 · 2019: 53 · 2018: 59 · 2017: 46 · 2016: 59 · 2015: 69 · 2014: 76 · 2013: 89 · 2012: 105
FWCI: 27.84
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
Locations: Trends in Biochemical Sciences (publishedVersion)
PubMed (publishedVersion)
Funders: Ministry of Education, Culture, Sports, Science and Technology
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: protein sorting signals, subcellular localization prediction, protein localization, signal peptide, amino acid composition, protein function prediction
MeSH terms: Algorithms, Proteins, Software, Subcellular Fractions, Protein Sorting Signals

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PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization

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