The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Using PSORT II, a program for predicting protein subcellular localization sites22, no putative NLS was identified in CRBN; however, CRBN was predicated to be nuclear using both PSORT II and PredictNLS.”
From Genome-wide screening reveals a role for subcellular localization of CRBN in the anti-myeloma activity of pomalidomide (2020) · cites this paper as [22]
In the citing paper
“Using PSORT II, a program for predicting protein subcellular localization sites22, no putative NLS was identified in CRBN; however, CRBN was predicated to be nuclear using both PSORT II and PredictNLS.”
From Genome-wide screening reveals a role for subcellular localization of CRBN in the anti-myeloma activity of pomalidomide (2020) · cites this paper as [22]
Citations
Cites
A new method for predicting signal sequence cleavage sites
von HEIJNE, G. (1986) · Nucleic Acids Research · doi:10.1093/nar/14.11.4683 · Cited by 4,473
Predicting coiled coils from protein sequences.
Lupas, A., Van Dyke, M., & Stock, J. (1991) · Science · doi:10.1126/science.252.5009.1162 · Cited by 3,953
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998
Bairoch, A. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.38 · Cited by 3,275
The PROSITE database, its status in 1995
Bairoch, A., Bücher, P., & Hofmann, K. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.1.189 · Cited by 1,916
A knowledge base for predicting protein localization sites in eukaryotic cells
Nakai, K., & Kanehisa, M. I. (1992) · Genomics · doi:10.1016/s0888-7543(05)80111-9 · Cited by 1,512
Self-citationThe detection and classification of membrane-spanning proteins
Klein, P., Kanehisa, M. I., & DeLisi, C. (1985) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/0005-2736(85)90375-x · Cited by 841
Expert system for predicting protein localization sites in gram‐negative bacteria
Nakai, K., & Kanehisa, M. I. (1991) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340110203 · Cited by 756
Self-citationUsing neural networks for prediction of the subcellular location of proteins
Reinhardt, A. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.9.2230 · Cited by 597
Predicting the orientation of eukaryotic membrane-spanning proteins.
Hartmann, E., Rapoport, T. A., & Lodish, H. F. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.15.5786 · Cited by 581
Relation between amino acid composition and cellular location of proteins 1 1Edited by F. E. Cohen
Cedano, J. A., Aloy, P., Perez-Pons, J. A., & Querol, E. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0804 · Cited by 397
Research works printed but not linked: 4
- 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
Cited by
Sorted by citations
Items 101–200 of 1,002
The pathway for perception and transduction of low‐temperature signals in Synechocystis
Suzuki, I., Los, D. A., Kanesaki, Y., Mikami, K., & Murata, N. (2000) · The EMBO Journal · doi:10.1093/emboj/19.6.1327 · Cited by 270
“An analysis using computer programs that predict the localization of proteins, such as PSORT (Nakai and Horton, 1999) and HMMTOP (Tusnady and Simon, 1998), indicated that Hik33 has two hydrophobic helices that might, in theory, span the membrane.”
MethodBujalka, H., Koenning, M., Jackson, S., Perreau, V. M., Pope, B., Hay, C. M., Mitew, S., Hill, A. F., Lu, Q. R., Wegner, M., et al. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001625 · Cited by 271
“The UniProt mouse MYRF sequence (accession number Q3UR85) was submitted to several subcellular targeting motif and feature predictors including ELM [46], PSORTII [47], NucPred [48], TMPRED [49], HMMTOP [50], Das-TMfilter [51], Toppred II [52], Paircoil2 [53], and to the protein databases PFAM [54] and Prosite [55].”
MethodKaryopherin-mediated nucleocytoplasmic transport
Wing, C. E., Fung, H. Y. J., & Chook, Y. M. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00446-7 · Cited by 272
The complex structures of arabinogalactan-proteins and the journey towards understanding function
Gaspar, Y. M., Johnson, K. L., McKenna, J. A., Bacic, A., & Schultz, C. J. (2001) · Plant Molecular Biology · doi:10.1023/a:1010683432529 · Cited by 270
“(Nakai and Horton, 1999) and big-PI predictor (Eisenhaber et al.”
MethodAutomatic prediction of protein function
Wrzeszczyński, K. O., Ofran, Y., Rost, B., Nair, R. P., & Liu, J. (2003) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-003-3114-8 · Cited by 269
Identification and characterization of a mitochondrial thioredoxin system in plants
Laloi, C., Rayapuram, N., Chartier, Y., Grienenberger, J. M., Bonnard, G., & Meyer, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.241340898 · Cited by 271
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants
Baets, G. D., Durme, J. V., Reumers, J., Maurer‐Stroh, S., Vanhee, P., Dopazo, J., Schymkowitz, J. W. H., & Rousseau, F. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr996 · Cited by 270
“PSORT (23) provides a prediction on the sub-cellular localization.”
BackgroundPark, S., Juliana, C. A., Hong, S., Datta, P., Hwang, I., Fernandes‐Alnemri, T., Yu, J., & Alnemri, E. S. (2013) · The Journal of Immunology · doi:10.4049/jimmunol.1301170 · Cited by 275
“A PSORT analysis (31) of the mouse NLRP3 N terminus similar to that performed by Subramanian et al.”
MethodOrigin and evolution of the Notch signalling pathway: an overview from eukaryotic genomes
Gazave, E., Lapébie, P., Richards, G. S., Brunet, F., Ereskovsky, A. V., Degnan, B. M., Borchiellini, C., Vervoort, M., & Renard, E. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-249 · Cited by 276
“In addition, for Notch, Delta and Jagged genes we used PSORTII [128] and PESTfind [129] software for identifying the nuclear localisation signal (NLS) and the PEST region respectively.”
MethodRichman, A. S., Swanson, A., Humphrey, T., et al. (2004) · The Plant Journal · doi:10.1111/j.1365-313x.2004.02275.x · Cited by 263
“, 2001), PSORT to predict sub-cellular localization (Nakai and Horton, 1999) and SignalP to predict signal peptides (Nielsen et al.”
BackgroundMethodKatayama, T., Sakuma, A., Kimura, T., Makimura, Y., Hiratake, J., Sakata, K., Yamanoi, T., Kumagai, H., & Yamamoto, K. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.15.4885-4893.2004 · Cited by 263
“jp) (24) programs revealed the presence of a signal peptide and a membrane anchor at the N and C termini, respectively.”
Background14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma
Lee, C., Ou, W., Mariño‐Enríquez, A., Zhu, M. J., Mayeda, M., Wang, Y., Guo, X., Brunner, A. L., Amant, F. C., French, C. A., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1115528109 · Cited by 260
How Evolutionary Pressure Against Protein Aggregation Shaped Chaperone Specificity
Rousseau, F., Serrano, L. G., & Schymkowitz, J. W. H. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.11.035 · Cited by 263
Chou, K., & Shen, H. (2006) · Journal of Proteome Research · doi:10.1021/pr060167c · Cited by 253
AY-WB Phytoplasma Secretes a Protein That Targets Plant Cell Nuclei
Bai, X., Correa, V. R., Toruño, T. Y., Ammar, E., Kamoun, S., & Hogenhout, S. A. (2008) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-22-1-0018 · Cited by 251
Lin, W., Fang, J., Xiao, X., et al. (2013) · Molecular BioSystems · doi:10.1039/c3mb25466f · Cited by 251
Evolutionary genomics of Salmonella : Gene acquisitions revealed by microarray analysis
Porwollik, S., Wong, R. M.-Y., & McClelland, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.122153699 · Cited by 249
Ishizaki, K., Larson, T. R., Schauer, N., Fernie, A. R., Graham, I. A., & Leaver, C. J. (2005) · The Plant Cell · doi:10.1105/tpc.105.035162 · Cited by 244
“The N-terminal sequence of the Arabidopsis ETFQO protein has characteristics consistent with that of a mitochondrial transit peptide and is predicted to target ETFQO to the mitochondrion by the three targeting prediction programs Predotar (http:// genoplante-info.infobiogen.fr/predotar/), MitoProt II (Claros and Vince…”
BackgroundHum-PLoc: A novel ensemble classifier for predicting human protein subcellular localization
Chou, K., & Shen, H. (2006) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2006.06.059 · Cited by 248
Identification of New Intrinsic Proteins in Arabidopsis Plasma Membrane Proteome
Marmagne, A., Rouet‐Mayer, M., Ferro, M., et al. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400001-mcp200 · Cited by 246
“All the GTP-binding proteins found here show a putative site of prenylation in their C-terminus, and the two ADP-ribosylation factors are predicted to be myristoylated (83, 84 ).”
BackgroundRissoan, M., Duhen, T., Bridon, J., Bendriss‐Vermare, N., Péronne, C., Vis, B. D. S., Brière, F., & Bates, E. E. M. (2002) · Blood · doi:10.1182/blood-2002-02-0638 · Cited by 251
Signal-3L: A 3-layer approach for predicting signal peptides
Shen, H., & Chou, K. (2007) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2007.08.140 · Cited by 241
“Actually, during the last two decades many efforts have been made in this regard [4–21].”
BackgroundSedbrook, J. C., Carroll, K. L., Hung, K. F., et al. (2002) · The Plant Cell · doi:10.1105/tpc.002360 · Cited by 240
“The computer program SignalP version 2.0 (http:// www.cbs.dtu.dk/services/SignalP-2.0/; Nielsen et al., 1997) predicted that all of these hydrophobic sequences were cleavable signal sequences, whereas PSORT (http://psort. nibb.ac.jp/form.html; Nakai and Horton, 1999) predicted that all but two of…”
BackgroundInfluentialMembrane Protein Structure: Prediction versus Reality
Elofsson, A., & von HEIJNE, G. (2007) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.76.052705.163539 · Cited by 239
Prediction of protein subcellular locations using fuzzy k-NN method
Huang, Y., & Li, Y. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg366 · Cited by 238
“This approach was integrated eventually into PSORT prediction system (Nakai and Horton, 1999).”
MethodMesd Encodes an LRP5/6 Chaperone Essential for Specification of Mouse Embryonic Polarity
Hsieh, J.-C., Lee, L., Zhang, L., Wefer, S., Brown, K., DeRossi, C., Wines, M. E., Rosenquist, T., & Holdener, B. C. (2003) · Cell · doi:10.1016/s0092-8674(03)00045-x · Cited by 237
Candat, A., Paszkiewicz, G., Neveu, M., Gautier, R., Logan, D. C., Avelange‐Macherel, M., & Macherel, D. (2014) · The Plant Cell · doi:10.1105/tpc.114.127316 · Cited by 241
“able online programs: PSORT (http://psort.hgc.jp/form.html; Nakai and Horton, 1999), MultiLoc (http://abi.”
BackgroundMethodInfluentialZahedi, R. P., Sickmann, A., Boehm, A., Winkler, C., Zufall, N., Schönfisch, B., Guiard, B., Pfanner, N., & Meisinger, C. (2006) · Molecular Biology of the Cell · doi:10.1091/mbc.e05-08-0740 · Cited by 234
“Three of the proteins, Yjl133c-a, Yhr198c, and Ygr207c, were predicted to contain a characteristic mitochondrial presequence in all three programs (Supplemental Table 6; Nakai and Horton, 1999; Guda et al., 2004; Small et al., 2004), indicating that they belong to the group of internal proteins accumulated as precurso…”
BackgroundThe Classical Arabinogalactan Protein Gene Family of Arabidopsis
Schultz, C., Johnson, K. L., Currie, G., & Bacic, A. (2000) · The Plant Cell · doi:10.1105/tpc.12.9.1751 · Cited by 242
“GPI-anchored, according to PSORT prediction of cellular localization (Nakai and Horton, 1999).”
BackgroundMethodInfluentialJohnston, J. B., Barrett, J. W., Nazarian, S. H., Goodwin, M., Ricuttio, D., Wang, G., & McFadden, G. (2005) · Immunity · doi:10.1016/j.immuni.2005.10.003 · Cited by 232
“Cell sorting predictions for M13L-PYD was carried out using PSORT II (Nakai and Horton, 1999), which determines the likelihood of the presence of a signal peptide and subcellular localization.”
MethodBlonder, J., Goshe, M. B., Moore, R. J., Paša‐Tolić, L., Masselon, C., Lipton, M. S. W., & Smith, R. D. (2002) · Journal of Proteome Research · doi:10.1021/pr0255248 · Cited by 231
Wiese, S., Gronemeyer, T., Ofman, R., Kunze, M., Grou, C. P., Almeida, J. A., Eisenacher, M., Stephan, C., Hayen, H., Schollenberger, L., et al. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700169-mcp200 · Cited by 231
“Only four candidates (ZADH2, ACAD11, ABHD14B, and a protein similar to BACAT) contain a peroxisomal targeting signal type 1 (PTS1) as predicted by using PSORT (58).”
MethodA complete survey of Trichoderma chitinases reveals three distinct subgroups of family 18 chitinases
Seidl, V., Huemer, B., Seiboth, B., et al. (2005) · FEBS Journal · doi:10.1111/j.1742-4658.2005.04994.x · Cited by 230
NEJ1 controls non-homologous end joining in Saccharomyces cerevisiae
Valencia‐Burton, M., Bentele, M., Vaze, M. B., Herrmann, G., Kraus, E., Lee, S. E., Schär, P., & Haber, J. E. (2001) · Nature · doi:10.1038/414666a · Cited by 228
“The amino-acid sequence of Nej1 predicts two transmembrane helices in the amino-terminal domain, so that it might be located in a nuclear membrane compartment or in the cytoplas”
BackgroundRohila, J. S., Chen, M. Y., Cerny, R. L., & Fromm, M. (2004) · The Plant Journal · doi:10.1111/j.1365-313x.2004.02031.x · Cited by 227
Schultz, C. J., Rumsewicz, M. P., Johnson, K. L., et al. (2002) · PLANT PHYSIOLOGY · doi:10.1104/pp.003459 · Cited by 227
“Professor Stanton B. Gelvin’s group (Purdue University, West Lafayette) identified the rat1 (resistant to Agrobacterium transformation) phenotype (Nam et al., 1999) in the same Feldman line that our group identified a T-DNA insertion in the promoter of AtAGP17 (Gaspar et al., 2001).”
BackgroundGene knockdown by RNAi in the pea aphid Acyrthosiphon pisum
Jaubert‐Possamai, S., Trionnaire, G. L., Bonhomme, J., Christophides, G. K., Rispe, C., & Tagu, D. (2007) · BMC Biotechnology · doi:10.1186/1472-6750-7-63 · Cited by 234
“Secretion signal peptide of 20 AA predicted by PSORTII [20] is bold, endoplasmic reticulum retention peptide "HDEL" is italicised, signature motifs of the calreticulin family are in black boxes, conserved repeated calreticulin sequences are in grey boxes.”
Gabaldón, T., Rainey, D. Y., & Huynen, M. A. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.02.067 · Cited by 224
Zheng, L., Zhou, M., Guo, Z., Lu, H., Qian, L., Dai, H., Qiu, J., Yakubovskaya, E., Bogenhagen, D. F., Demple, B., et al. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.09.024 · Cited by 222
“The classic Pat4, Pat7, and bipartite nuclear localization signals were identified with the pSORT II program (Nakai and Horton, 1999).”
MethodIsolation of a cDNA Representing the Fanconi Anemia Complementation Group E Gene
de Winter, J. P., Léveillé, F., van Berkel, C. G. M., Rooimans, M. A., van der Weel, L., Steltenpool, J., Demuth, I., Morgan, N. V., Alon, N., Bosnoyan-Collins, L., et al. (2000) · The American Journal of Human Genetics · doi:10.1016/s0002-9297(07)62959-0 · Cited by 221
“Nuclear localization signals as predicted by PSORT II (Nakai and Horton, 1999) are shown in bold and”
MethodLarge‐scale plant protein subcellular location prediction
Chou, K., & Shen, H. (2006) · Journal of Cellular Biochemistry · doi:10.1002/jcb.21096 · Cited by 221
“Many methods have been developed in this regard [Nakashima and Nishikawa, 1994; Cedano et al., 1997; Chou and Elrod, 1999; Nakai and Horton, 1999; Emanuelsson et al., 2000; Nakai, 2000; Feng, 2001; Chou and Cai, 2002; Feng, 2002; Pan et al., 2003; Zhou and Doctor, 2003; Garg et al., 2005; Matsuda…”
MethodThermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus
Takami, H., Takaki, Y., Chee, G.-J., et al. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh970 · Cited by 221
“For calculating the amino acid composition, proteins containing at least two transmembrane segments, as predicted by the PSORT program (22), were also eliminated.”
MethodPark, C., Peng, Y., Chen, X., Dardick, C. D., Ruan, D., Bart, R. S., Canlas, P. E., & Ronald, P. C. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060231 · Cited by 214
“org/) [61], XB15 has a putative nuclear-localization sequence (Figure 2) and is predicted to be a nuclear protein.”
BackgroundIntegrative Analysis of the Mitochondrial Proteome in Yeast
Prokisch, H., Scharfe, C., Camp, D., Xiao, W., David, L., Andréoli, C., Monroe, M. E., Moore, R., Gritsenko, M. A., Kozany, C., et al. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020160 · Cited by 219
“…studies (Uetz et al. 2000; Ito et al. 2001; Gavin et al. 2002; Ho et al. 2002), mass spectrometry (MS) of mitochondria (Pflieger et al. 2002; Ohlmeier et al. 2003), and various computational predictions of mitochondrial proteins (Nakai and Horton 1999; Drawid and Gerstein 2000; Small et al. 2004).”
BackgroundGiglione, C., Serero, A., Pierre, M., Boisson, B., & Meinnel, T. (2000) · EMBO Journal · doi:10.1093/emboj/19.21.5916 · Cited by 210
Localizing proteins in the cell from their phylogenetic profiles
Marcotte, E. M., Xénarios, I., van der Bliek, A. M., & Eisenberg, D. S. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.220399497 · Cited by 216
Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT
Chen, Y., Yu, P., Luo, J., & Jiang, Y. (2003) · Mammalian Genome · doi:10.1007/s00335-003-2296-6 · Cited by 217
“Computational approaches have been applied to secreted protein and signal peptide prediction, such as PSORT (Horton and Nakai 1997; Nakai and Horton 1999), SignalP (Nielsen et al. 1997, 1999), TargetP (Emanuelsson et al. 2000), Sigcleave (Jagla and Schuchhardt 2000), PHYSEAN (Ladunga 1999).”
MethodRalph, S. G., Park, J., Bohlmann, J., & Mansfield, S. D. (2006) · Plant Molecular Biology · doi:10.1007/s11103-005-2226-y · Cited by 215
“01 (Emanuelsson et al., 2000) and PSORT (Nakai and Horton, 1999) subcellular localization software, we predict that all 17 full-length and one near full-length (PDIR4) spruce DIR proteins are targeted to the secretory pathway, either through the default pathway for extracellular release, or…”
BackgroundInfluentialPrediction of Peroxisomal Targeting Signal 1 Containing Proteins from Amino Acid Sequence
Neuberger, G., Maurer‐Stroh, S., Eisenhaber, B., Hartig, A., & Eisenhaber, F. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00319-x · Cited by 213
Lipoprotein computational prediction in spirochaetal genomes
Setúbal, J. C., Reis, M. S., Matsunaga, J., & Haake, D. A. (2005) · Microbiology · doi:10.1099/mic.0.28317-0 · Cited by 212
“We compared the performance of the SpLip, Psort (Nakai & Horton, 1999) and LipoP (Juncker et al., 2003) algorithms.”
MethodAnalysis of rice glycosyl hydrolase family 1 and expression of Os4bglu12 β-glucosidase
Opassiri, R., Pomthong, B., Onkoksoong, T., et al. (2006) · BMC Plant Biology · doi:10.1186/1471-2229-6-33 · Cited by 212
“Cellular locations of predicted proteins were predicted by PSORT [ 67 ], signal sequences were predicted by SignalP [68], N-glycosylation sites were predicted by NetNGlyc, and the molecular weights (MW) and isoelectric points (pI) of the proteins were predicted by ProtParam at the Expasy proteomics server [69].”
MethodSystematic functional profiling of transcription factor networks in Cryptococcus neoformans
Jung, K., Yang, D., Maeng, S., Lee, K.-T., So, Y.-S., Hong, J., Choi, J., Byun, H.-J., Kim, H., Bang, S., et al. (2015) · Nature Communications · doi:10.1038/ncomms7757 · Cited by 209
Mating-Type Structure, Evolution, and Function in Euascomycetes
Debuchy, R., & Turgeon, B. G. (2006) · Springer eBooks · doi:10.1007/3-540-28135-5_15 · Cited by 202
“teins (PSORT II, Nakai and Horton 1999 ) does not detect any nuclear localization signal and predicts a cytoplasmic localization.”
BackgroundCellular and subcellular localization of PDE10A, a striatum-enriched phosphodiesterase
Zhi, X., Adamowicz, W. O., Eldred, W. D., et al. (2006) · Neuroscience · doi:10.1016/j.neuroscience.2005.12.042 · Cited by 198
“A single potential transmembrane region for rat PDE10A2, at amino acids 198-214, is predicted by the PSORT program for subcellular localization signals (Nakai and Horton, 1999).”
BackgroundZhicheng, W., Xiao, X., & Chou, K. (2011) · Molecular BioSystems · doi:10.1039/c1mb05232b · Cited by 198
Evolution of the Isoprene Biosynthetic Pathway in Kudzu
Sharkey, T. D., Yeh, S., WIBERLEY, A. E., Falbel, T. G., Gong, D., & Fernandez, D. E. (2005) · PLANT PHYSIOLOGY · doi:10.1104/pp.104.054445 · Cited by 198
“PSORT (Nakai and Horton, 1999; http://psort.ims.u-tokyo.ac.jp/), TargetP (Nielsen et al., 1997; Emanuelsson et al., 2000; http://www.cbs.dtu.dk/services/), and ChloroP (Emanuelsson et al., 1999; http://www.cbs.dtu.dk/services/ChloroP/) were used to identify possible targeting sequences in the gene…”
MethodInfluentialThe family of DOF transcription factors: from green unicellular algae to vascular plants
Moreno-Risueno, M. Á., Martínez, M., Vicente‐Carbajosa, J., & Carbonero, P. (2006) · Molecular Genetics and Genomics · doi:10.1007/s00438-006-0186-9 · Cited by 198
“Conserved motifs identiWed by MEME were scanned using WoLF PSORT (Nakai and Horton 1999) at PSORT server (http://”
MethodEguchi, T., Kubota, S., Kawata, K., Mukudai, Y., Uehara, J., Ohgawara, T., Ibaragi, S., Sasaki, A., Kuboki, T., & Takigawa, M. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.01288-07 · Cited by 197
“The bindings of HP1 , NF45, NCoR1, and CAFp48 to MMP3 were confirmed from the results of a GST pull-down assay (Fig.”
BackgroundMethodInfluentialNAD Kinase Levels Control the NADPH Concentration in Human Cells
Pollak, N., Niere, M., & Ziegler, M. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m704442200 · Cited by 205
Very-long-chain Acyl-CoA Synthetases
Watkins, P. A. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.r700037200 · Cited by 199
Shen, H., & Chou, K. (2007) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2007.02.071 · Cited by 196
“Actually, various different approaches for predicting protein subcellular location have been proposed [3–18].”
MethodNovel Family of Sensor Histidine Kinase Genes in Arabidopsis thaliana
Ueguchi, C., Koizumi, H., Suzuki, T., et al. (2001) · Plant and Cell Physiology · doi:10.1093/pcp/pce015 · Cited by 196
The plant mitochondrial proteome
Millar, A. H., Heazlewood, J. L., Kristensen, B. K., et al. (2004) · Trends in Plant Science · doi:10.1016/j.tplants.2004.12.002 · Cited by 196
Tong, W.-H., Jameson, G. N. L., Huynh, B. H., & Rouault, T. A. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1732541100 · Cited by 194
The nuclear envelope proteome differs notably between tissues
Korfali, N., Wilkie, G. S., Swanson, S. K., Sršeň, V., Heras, J. I. D. L., Batrakou, D. G., Malik, P. R., Zuleger, N., Kerr, A. R. W., Florens, L. A., et al. (2012) · Nucleus · doi:10.4161/nucl.22257 · Cited by 195
Importin α‐regulated nucleation of microtubules by TPX2
Schatz, C., Santarella, R. A., Hoenger, A., Karsenti, E., Mattaj, I. W., Gruß, O. J., & Salas, R. E. C. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg195 · Cited by 195
Searching for hypothetical proteins: Theory and practice based upon original data and literature
Lübec, G., Afjehi‐Sadat, L., Yang, J., & John, J. P. P. (2005) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2005.10.001 · Cited by 193
SPD--a web-based secreted protein database
Chen, Y. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki093 · Cited by 196
Gene encoding a new RING-B-box-Coiled-coil protein is mutated in mulibrey nanism
Avela, K., Lipsanen‐Nyman, M., Idänheimo, N., Seemanová, E., Rosengren, S. S., Mäkelä, T. P., Perheentupa, J., de la Chapelle, A., & Lehesjoki, A. (2000) · Nature Genetics · doi:10.1038/77053 · Cited by 189
Christinet, L., Burdet, F., Zaiko, M., Hinz, U. G., & Zrÿd, J. (2004) · PLANT PHYSIOLOGY · doi:10.1104/pp.103.031914 · Cited by 192
“PSORTII tool (Nakai and Horton, 1999) predicts a clear cytoplasmic localization of the protein.”
MethodCurwen, R. S., Ashton, P. D., Sundaralingam, S., et al. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500313-mcp200 · Cited by 190
“PSORT II (20) was used to determine whether proteins contained any transmembrane domains.”
MethodSalusins: newly identified bioactive peptides with hemodynamic and mitogenic activities
Shichiri, M., Ishimaru, S., Ota, T., Nishikawa, T., Isogai, T., & Hirata, Y. (2003) · Nature Medicine · doi:10.1038/nm913 · Cited by 191
Richly, E., & Leister, D. (2004) · Gene · doi:10.1016/j.gene.2004.01.008 · Cited by 189
“Accuracy of cTP predictors and of their combinations The specificity and sensitivity of the four cTP predictors iPSORT (Bannai et al., 2002), TargetP (Emanuelsson et al., 2000), PCLR (Schein et al., 2001) and Predotar (http:// www.inra.fr/predotar/) have been determined based on a test set of 4500 proteins whose subce…”
MethodInfluentialTurner, G. W., & Croteau, R. (2004) · PLANT PHYSIOLOGY · doi:10.1104/pp.104.050229 · Cited by 189
“…targeting motifs with the following prediction programs: TargetP (Emanuelsson et al., 2000), ChloroP (Emanuelsson et al., 1999), and PSORT (Nakai and Horton, 1999), all available through the ExPASy (Expert Protein Analysis System) proteomics server (http://us.expasy.org/) sponsored by the…”
BackgroundMethodInfluentialItabashi, E., Iwata, N., Fujii, S., Kazama, T., & Toriyama, K. (2010) · The Plant Journal · doi:10.1111/j.1365-313x.2010.04427.x · Cited by 185
Prediction of organellar targeting signals
Emanuelsson, O., & von HEIJNE, G. (2001) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/s0167-4889(01)00145-8 · Cited by 182
The COBRA Family of Putative GPI-Anchored Proteins in Arabidopsis. A New Fellowship in Expansion
Roudier, F., Schindelman, G., DeSalle, R., & Benfey, P. N. (2002) · PLANT PHYSIOLOGY · doi:10.1104/pp.007468 · Cited by 185
“More recently, forward and reverse genetic approaches have led to the identification of new classes of cell wall modifiers such as cellulose synthases (Arioli et al., 1998; Fagard et al., 2000), endo- -1,4- glucanases (Nicol et al., 1998), and wall-associated kinases (Kohorn, 2001).”
BackgroundShen, H., & Chou, K. (2010) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2010.01.018 · Cited by 181
“, the predictors called ‘‘PSORT’’ (Nakai, 2000; Nakai and Kanehisa, 1991; Nakai and Horton, 1999), ‘‘PSORT-B’’ (Gardy et al.”
Distribution and diversity of phytate-mineralizing bacteria
Lim, B. L., Yeung, P., Cheng, C.-W., & Hill, J. E. (2007) · The ISME Journal · doi:10.1038/ismej.2007.40 · Cited by 183
“Expectedly, these phytases are predicted to be exported to the membrane or to the periplasmic space by the PSORT program (Nakai and Horton, 1999).”
BackgroundMethodShen, H., & Chou, K. (2005) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2005.06.087 · Cited by 180
Golden, T. A., Schauer, S. E., Lang, J. D., et al. (2002) · PLANT PHYSIOLOGY · doi:10.1104/pp.003491 · Cited by 179
“NLS was detected using the PSORT server (Nakai and Horton, 1999).”
MethodDatta, V., Myskowski, S. M., Kwinn, L. A., Chiem, D. N., Varki, N. M., Kansal, R. G., Kotb, M., & Nizet, V. (2005) · Molecular Microbiology · doi:10.1111/j.1365-2958.2005.04583.x · Cited by 176
“Without significant GenBank homologies to genes of known function, sagC and sagF are predicted to be membrane proteins, and sagD a cytoplasmic protein, by the PSORT localization algorithm ( Nakai and Horton, 1999 ).”
BackgroundBlee, K. A., Choi, J. W., O’Connell, A. P., et al. (2003) · Phytochemistry · doi:10.1016/s0031-9422(03)00212-7 · Cited by 178
In Vivo Substrate Specificity of Periplasmic Disulfide Oxidoreductases
Hiniker, A. O., & Bardwell, J. C. A. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m311391200 · Cited by 178
Differential gene expression of rice in response to silicon and rice blast fungus Magnaporthe oryzae
Brunings, A. M., Datnoff, L. E., Ma, J., et al. (2009) · Annals of Applied Biology · doi:10.1111/j.1744-7348.2009.00347.x · Cited by 177
Embeddings from deep learning transfer GO annotations beyond homology
Littmann, M., Heinzinger, M., Dallago, C., Olenyi, T., & Rost, B. (2021) · Scientific Reports · doi:10.1038/s41598-020-80786-0 · Cited by 176
Shimomura, Y., Harada, M., Goto, M., Sugo, T., Matsumoto, Y., Abe, M., Watanabe, T., Asami, T., Kitada, C., Mori, M., et al. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m205337200 · Cited by 174
Bakker, B. M., Bro, C., Kötter, P., Luttik, M. A. H., van Dijken, J. P., & Pronk, J. T. (2000) · Journal of Bacteriology · doi:10.1128/jb.182.17.4730-4737.2000 · Cited by 171
“According to the program PSORT II (21, 22), four of these, Yal060w, Yal061w, Adh4, and Ydl114w, have a substantial probability (30 to 45%) of being mitochondrial.”
MethodZhou, Y., Zeng, L., Liu, X., Gui, J., Mei, X., Fu, X., Dong, F., Tang, J., Zhang, L., & Yang, Z. (2017) · Food Chemistry · doi:10.1016/j.foodchem.2017.03.122 · Cited by 172
Fuzzy KNN for predicting membrane protein types from pseudo-amino acid composition
Shen, H., Yang, J., & Chou, K. (2005) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2005.08.016 · Cited by 174
Role of Saccharomyces cerevisiae ISA1 and ISA2 in Iron Homeostasis
Jensen, L. T., & Culotta, V. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.11.3918-3927.2000 · Cited by 173
“(31), a potential sequence for mitochondrial targeting occurs with the first 31 residues of the protein, followed by an additional 25 amino acids that could not be fitted to any consensus sequence (Fig.”
BackgroundMethodNanni, L., & Lumini, A. (2008) · Amino Acids · doi:10.1007/s00726-007-0018-1 · Cited by 172
“…sequence (Cai et al. 2000, 2002; Cedano et al. 1997; Chou 2001; Chou and Cai 2002, 2003, 2004a, b; Chou and Elrod 1998, 1999; Chou and Shen 2006; Nakai and Horton 1999; Nakai and Kanehisa 1992; Yuan 1999) as well as the relevant references cited in a recent review article (Chou and Shen 2007d).”
BackgroundMethodFunctional properties of multiple isoforms of human divalent metal-ion transporter 1 (DMT1)
Mackenzie, B., Takanaga, H., Hubert, N., Rolfs, A., & Hediger, M. A. (2007) · Biochemical Journal · doi:10.1042/bj20061290 · Cited by 173
Yadav, S. K., & Guleria, P. (2012) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2010.519447 · Cited by 172
“Using the prediction program PSORT, KO has been found to be localized at the membrane of endoplasmic reticulum (Nakai and Horton, 1999).”
MethodDomergue, F., Lerchl, J., Zähringer, U., & Heinz, E. (2002) · European Journal of Biochemistry · doi:10.1046/j.1432-1033.2002.03104.x · Cited by 168
“In good agreement with this model, the program developed by Nakai & Horton for prediction of cellular localization [34] indicated that both proteins were localized in the endoplasmic reticulum, although no di-lysine retention signal was present in the sequences.”
MethodFierens, E., Rombouts, S., Gebruers, K., et al. (2007) · Biochemical Journal · doi:10.1042/bj20061291 · Cited by 171
“The tlxi gene contains no introns and encodes a mature protein of 151 amino acids preceded by a signal sequence of 26 amino acids (PSORT [27]).”
BackgroundMolecular Basis for Mycophenolic Acid Biosynthesis in Penicillium brevicompactum
Regueira, T. B., Kildegaard, K. R., Hansen, B. G., Mortensen, U. H., Hertweck, C., & Nielsen, J. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.03015-10 · Cited by 171
“A PSORT II analysis (34) of the amino acid sequence of MpaH identified a PTS1-like tripeptide GKL at the C-terminal end of this protein, suggesting that MpaH may be located in the peroxisomes.”
MethodEnergy crisis: The role of oxidative phosphorylation in acute inflammation and sepsis
Lee, I., & Hüttemann, M. (2014) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2014.05.031 · Cited by 176
Shen, H., & Chou, K. (2009) · Analytical Biochemistry · doi:10.1016/j.ab.2009.07.046 · Cited by 170
Redox Regulation of a Novel Plastid-Targeted β-Amylase of Arabidopsis
Sparla, F., Costa, A., Schiavo, F. L., Pupillo, P., & Trost, P. (2006) · PLANT PHYSIOLOGY · doi:10.1104/pp.106.079186 · Cited by 170
“To predict the presence of a putative transit peptide for localization into organelles, amino acid sequences were analyzed by ChloroP (Emanuelsson et al., 1999) and PSORT (Nakai and Horton, 1999).”
BackgroundMethodInfluential
Metadata
- Authors
- Nakai, K., & Horton, P.
- Affiliations
- The University of Osaka (JP)
- Corresponding author
- Nakai, Kenta
- Venue
- Trends in Biochemical Sciences
- Publisher
- Elsevier BV
- Published
- 1999-01
- Volume
- 24
- Issue
- 1
- Pages
- 34-35
- ISSN
- 0968-0004 (ISSN-L)
- 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
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
