The DOI matches its Crossref record.
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
Open accessAbstract
We have developed a new method for the identification of signal peptides and their cleavage sites based on neural networks trained on separate sets of prokaryotic and eukaryotic sequence. The method performs significantly better than previous prediction schemes and can easily be applied on genome-wide data sets. Discrimination between cleaved signal peptides and uncleaved N-terminal signal-anchor sequences is also possible, though with lower precision. Predictions can be made on a publicly available WWW server.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cited by
Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. L. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4315 · Cited by 12,654
Self-citationSignalP 4.0: discriminating signal peptides from transmembrane regions
Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H. (2011) · Nature Methods · doi:10.1038/nmeth.1701 · Cited by 8,847
Self-citationImproved Prediction of Signal Peptides: SignalP 3.0
Dyrløv Bendtsen, J., Nielsen, H., von Heijne, G., & Brunak, S. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.05.028 · Cited by 6,350
Self-citationThe hormone resistin links obesity to diabetes
Steppan, C. M., Bailey, S. T., Bhat, S., Brown, E. J., Banerjee, R. R., Wright, C. M., Patel, H. R., Ahima, R. S., & Lazar, M. A. (2001) · Nature · doi:10.1038/35053000 · Cited by 4,755
Genome sequence of the human malaria parasite Plasmodium falciparum
Gardner, M. J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R. W., Carlton, J. M., Pain, A., Nelson, K. E., Bowman, S., et al. (2002) · Nature · doi:10.1038/nature01097 · Cited by 4,407
The complete genome sequence of the gastric pathogen Helicobacter pylori
Tomb, J.-F., White, O., Kerlavage, A. R., Clayton, R. A., Sutton, G. G., Fleischmann, R. D., Ketchum, K. A., Klenk, H. P., Gill, S., Dougherty, B. A., et al. (1997) · Nature · doi:10.1038/41483 · Cited by 3,529
Assessing the accuracy of prediction algorithms for classification: an overview
Baldi, P., Brunak, S., Chauvin, Y., Andersen, C. A. F., & Nielsen, H. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.5.412 · Cited by 2,111
Self-citationLEAP-1, a novel highly disulfide-bonded human peptide, exhibits antimicrobial activity
Krause, A., Neitz, S., Mägert, H.-J., Schulz, A., Forssmann, W.-G., Schulz-Knappe, P., & Adermann, K. (2000) · FEBS Letters · doi:10.1016/s0014-5793(00)01920-7 · Cited by 1,324
Brogiolo, W., Stocker, H., Ikeya, T., Rintelen, F., Fernandez, R., & Hafen, E. (2001) · Current Biology · doi:10.1016/s0960-9822(01)00068-9 · Cited by 1,255
An Apolipoprotein Influencing Triglycerides in Humans and Mice Revealed by Comparative Sequencing
Pennacchio, L. A., Olivier, M., Hubacek, J. A., Cohen, J. C., Cox, D. R., Fruchart, J.-C., Krauss, R. M., & Rubin, E. M. (2001) · Science · doi:10.1126/science.1064852 · Cited by 921
Identification of a novel FGF, FGF-21, preferentially expressed in the liver
Nishimura, T., Nakatake, Y., Konishi, M., & Itoh, N. (2000) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/s0167-4781(00)00067-1 · Cited by 847
Polyphosphoprotein from the Adhesive Pads of Mytilus edulis
Waite, J. H., & Qin, X. (2001) · Biochemistry · doi:10.1021/bi002718x · Cited by 610
Protein Kinase G from Pathogenic Mycobacteria Promotes Survival Within Macrophages
Walburger, A., Koul, A., Ferrari, G., Nguyen, L., Prescianotto-Baschong, C., Huygen, K., Klebl, B., Thompson, C., Bacher, G., & Pieters, J. (2004) · Science · doi:10.1126/science.1099384 · Cited by 595
Comparing two K-category assignments by a K-category correlation coefficient
Gorodkin, J. (2004) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2004.09.006 · Cited by 545
Performance of mutation pathogenicity prediction methods on missense variants
Thusberg, J., Olatubosun, A., & Vihinen, M. (2011) · Human Mutation · doi:10.1002/humu.21445 · Cited by 537
A comprehensive review of signal peptides: Structure, roles, and applications
Owji, H., Nezafat, N., Negahdaripour, M., Hajiebrahimi, A., & Ghasemi, Y. (2018) · European Journal of Cell Biology · doi:10.1016/j.ejcb.2018.06.003 · Cited by 523
Frzb, a Secreted Protein Expressed in the Spemann Organizer, Binds and Inhibits Wnt-8
Wang, S., Krinks, M., Lin, K., Luyten, F. P., & Moos, M. (1997) · Cell · doi:10.1016/s0092-8674(00)81922-4 · Cited by 518
A novel member of a zinc transporter family is defective in acrodermatitis enteropathica
Wang, K., Zhou, B., Kuo, Y.-M., Zemansky, J., & Gitschier, J. (2002) · The American Journal of Human Genetics · doi:10.1086/341125 · Cited by 491
Sprouty, an intracellular inhibitor of Ras signaling
Casci, T., Vinós, J., & Freeman, M. (1999) · Cell · doi:10.1016/s0092-8674(00)80576-0 · Cited by 467
Paetzel, M., Karla, A., Strynadka, N. C. J., & Dalbey, R. E. (2002) · Chemical Reviews · doi:10.1021/cr010166y · Cited by 440
Anaerobic Microbial Dehalogenation
Smidt, H., & de Vos, W. M. (2004) · Annual Review of Microbiology · doi:10.1146/annurev.micro.58.030603.123600 · Cited by 434
Graaf, C. D., Donnelly, D., Wootten, D., Lau, J., Sexton, P. M., Miller, L. J., Ahn, J.-M., Liao, J., Fletcher, M. M., Yang, D., et al. (2016) · Pharmacological Reviews · doi:10.1124/pr.115.011395 · Cited by 403
Gan, P., Ikeda, K., Irieda, H., Narusaka, M., O'Connell, R. J., Narusaka, Y., Takano, Y., Kubo, Y., & Shirasu, K. (2013) · New Phytologist · doi:10.1111/nph.12085 · Cited by 379
Edens, W. A., Sharling, L., Cheng, G., Shapira, R., Kinkade, J. M., Lee, T., Edens, H. A., Tang, X., Sullards, C., Flaherty, D. B., et al. (2001) · The Journal of Cell Biology · doi:10.1083/jcb.200103132 · Cited by 375
The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria
Gey van Pittius, N. C., Gamieldien, J., Hide, W., Brown, G. D., Siezen, R. J., & Beyers, A. D. (2001) · Genome Biology · doi:10.1186/gb-2001-2-10-research0044 · Cited by 375
Anantharaman, V., & Aravind, L. (2003) · Genome Biology · doi:10.1186/gb-2003-4-2-r11 · Cited by 365
Kaplan, J. B., Ragunath, C., Ramasubbu, N., & Fine, D. H. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.16.4693-4698.2003 · Cited by 364
Sundstrom, P. (2002) · Cellular Microbiology · doi:10.1046/j.1462-5822.2002.00206.x · Cited by 336
Analysis of the proteome of Mycobacterium tuberculosis in silico
Tekaia, F., Gordon, S. V., Garnier, T., Brosch, R., Barrell, B. G., & Cole, S. T. (1999) · Tubercle and Lung Disease · doi:10.1054/tuld.1999.0220 · Cited by 311
An eight cysteine-containing CFEM domain unique to a group of fungal membrane proteins
Kulkarni, R. D., Kelkar, H. S., & Dean, R. A. (2003) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(03)00025-2 · Cited by 294
Genome-wide identification of fungal GPI proteins.
de Groot, P. W. J., Hellingwerf, K. J., & Klis, F. M. (2003) · Yeast · doi:10.1002/yea.1007 · Cited by 276
Identification of novel adrenomedullin in mammals: a potent cardiovascular and renal regulator
Takei, Y., Inoue, K., Ogoshi, M., Kawahara, T., Bannai, H., & Miyano, S. (2004) · FEBS Letters · doi:10.1016/s0014-5793(03)01368-1 · Cited by 268
CHLOROPLAST UNUSUAL POSITIONING1 Is Essential for Proper Chloroplast Positioning
Oikawa, K., Kasahara, M., Kiyosue, T., Kagawa, T., Suetsugu, N., Takahashi, F., Kanegae, T., Niwa, Y., Kadota, A., & Wada, M. (2003) · The Plant Cell · doi:10.1105/tpc.016428 · Cited by 258
Using subsite coupling to predict signal peptides
Chou, K.-C. (2001) · Protein Engineering, Design and Selection · doi:10.1093/protein/14.2.75 · Cited by 255
Zhang, L., Tian, L.-H., Zhao, J.-F., Song, Y., Zhang, C.-J., & Guo, Y. (2009) · Plant Physiology · doi:10.1104/pp.108.131144 · Cited by 246
Extensive identification and analysis of conserved small ORFs in animals
Mackowiak, S. D., Zauber, H., Bielow, C., Thiel, D., Kutz, K., Calviello, L., Mastrobuoni, G., Rajewsky, N., Kempa, S., Selbach, M., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0742-x · Cited by 227
A Comparative Genome Analysis Identifies Distinct Sorting Pathways in Gram-Positive Bacteria
Comfort, D., & Clubb, R. T. (2004) · Infection and Immunity · doi:10.1128/iai.72.5.2710-2722.2004 · Cited by 203
A Comprehensive Proteomics and Transcriptomics Analysis of Bacillus subtilis Salt Stress Adaptation
Hahne, H., Mäder, U., Otto, A., Bonn, F., Steil, L., Bremer, E., Hecker, M., & Becher, D. (2010) · Journal of Bacteriology · doi:10.1128/jb.01106-09 · Cited by 183
Maurel, P., Einheber, S., Galinska, J., Thaker, P., Lam, I., Rubin, M. B., Scherer, S. S., Murakami, Y., Gutmann, D. H., & Salzer, J. L. (2007) · The Journal of Cell Biology · doi:10.1083/jcb.200705132 · Cited by 177
Two Novel Heat-Soluble Protein Families Abundantly Expressed in an Anhydrobiotic Tardigrade
Yamaguchi, A., Tanaka, S., Yamaguchi, S., Kuwahara, H., Takamura, C., Imajoh-Ohmi, S., Horikawa, D. D., Toyoda, A., Katayama, T., Arakawa, K., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0044209 · Cited by 176
Cathelicidin family of antimicrobial peptides: Proteolytic processing and protease resistance
Shinnar, A. E., Butler, K. L., & Park, H. J. (2003) · Bioorganic Chemistry · doi:10.1016/s0045-2068(03)00080-4 · Cited by 170
Thompson, J. M., Jones, H. A., & Perry, R. D. (1999) · Infection and Immunity · doi:10.1128/iai.67.8.3879-3892.1999 · Cited by 154
Fernandez-Espla, M. D., Garault, P., Monnet, V., & Rul, F. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.11.4772-4778.2000 · Cited by 143
Wall, T., Båth, K., Britton, R. A., Jonsson, H., Versalovic, J., & Roos, S. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01502-06 · Cited by 131
Wright, D. J., Smith, S. C., Joardar, V., Scherer, S., Jervis, J., Warren, A., Helm, R. F., & Potts, M. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m505961200 · Cited by 130
Duan, Q. L., Nikpoor, B., Dubé, M.-P., Molinaro, G., Meijer, I. A., Dion, P., Rochefort, D., Saint-Onge, J., Flury, L., Brown, N. J., et al. (2005) · The American Journal of Human Genetics · doi:10.1086/496899 · Cited by 126
Tanaka, S., Tanaka, J., Miwa, Y., Horikawa, D. D., Katayama, T., Arakawa, K., Toyoda, A., Kubo, T., & Kunieda, T. (2015) · PLOS ONE · doi:10.1371/journal.pone.0118272 · Cited by 128
Carles, C. C., Choffnes-Inada, D., Reville, K., Lertpiriyapong, K., & Fletcher, J. C. (2005) · Development · doi:10.1242/dev.01642 · Cited by 128
Biochemistry and molecular biology of exocellular fungal β-(1,3)- and β-(1,6)-glucanases
Martin, K., McDougall, B. M., McIlroy, S., Jayus, Chen, J., & Seviour, R. J. (2007) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2006.00055.x · Cited by 127
Yeast wall protein 1 of Candida albicans
Granger, B. L., Flenniken, M. L., Davis, D. A., Mitchell, A. P., & Cutler, J. E. (2005) · Microbiology · doi:10.1099/mic.0.27663-0 · Cited by 126
Microbial stability of pharmaceutical and cosmetic products
Dao, H., Lakhani, P., Police, A., Kallakunta, V., Ajjarapu, S. S., Wu, K.-W., Ponkshe, P., Repka, M. A., & Narasimha Murthy, S. (2018) · AAPS PharmSciTech · doi:10.1208/s12249-017-0875-1 · Cited by 125
Syntrophic growth on Formate: a new microbial niche in anoxic environments
Dolfing, J., Jiang, B., Henstra, A. M., Stams, A. J. M., & Plugge, C. M. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.01428-08 · Cited by 124
Dainichi, T., Maekawa, Y., Ishii, K., Zhang, T., Nashed, B. F., Sakai, T., Takashima, M., & Himeno, K. (2001) · Infection and Immunity · doi:10.1128/iai.69.12.7380-7386.2001 · Cited by 125
Culi, J., & Mann, R. S. (2003) · Cell · doi:10.1016/s0092-8674(02)01279-5 · Cited by 119
Deep learning in biomedical data science
Baldi, P. (2018) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-080917-013343 · Cited by 119
Genomic evidence for mating abilities in the asexual pathogen Aspergillus fumigatus
Pöggeler, S. (2002) · Current Genetics · doi:10.1007/s00294-002-0338-3 · Cited by 115
Genomic Analysis of Caenorhabditis elegans Reveals Ancient Families of Retroviral-like Elements
Bowen, N. J., & McDonald, J. F. (1999) · Genome Research · doi:10.1101/gr.9.10.924 · Cited by 102
A Strategy for Discovery of Endocrine Interactions with Application to Whole-Body Metabolism
Seldin, M. M., Koplev, S., Rajbhandari, P., Vergnes, L., Rosenberg, G. M., Meng, Y., Pan, C., Phuong, T. M. N., Gharakhanian, R., Che, N., et al. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.03.015 · Cited by 84
Jankovic, I., Ventura, M., Meylan, V., Rouvet, M., Elli, M., & Zink, R. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.11.3288-3296.2003 · Cited by 82
Grevesse, C., Lepoivre, P., & Jijakli, M. H. (2003) · Phytopathology® · doi:10.1094/phyto.2003.93.9.1145 · Cited by 78
Cloning and expression of a novel, truncated, progesterone receptor
Saner, K. J., Welter, B. H., Zhang, F., Hansen, E., Dupont, B., Wei, Y., & Price, T. M. (2003) · Molecular and Cellular Endocrinology · doi:10.1016/s0303-7207(02)00380-5 · Cited by 64
Kajkowski, E. M., Lo, C. F., Ning, X., Walker, S., Sofia, H. J., Wang, W., Edris, W., Chanda, P., Wagner, E., Vile, S., et al. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m011161200 · Cited by 63
Assessing the bacterial contribution to the plastid proteome
Qiu, H., Price, D. C., Weber, A. P. M., Facchinelli, F., Yoon, H. S., & Bhattacharya, D. (2013) · Trends in Plant Science · doi:10.1016/j.tplants.2013.09.007 · Cited by 62
Calhoun, S., Bell, T. A. S., Dahlin, L. R., Kunde, Y., LaButti, K., Louie, K. B., Kuftin, A., Treen, D., Dilworth, D., Mihaltcheva, S., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-01859-y · Cited by 60
cDNA cloning and expression of human activin βE subunit
Hashimoto, O., Tsuchida, K., Ushiro, Y., Hosoi, Y., Hoshi, N., Sugino, H., & Hasegawa, Y. (2002) · Molecular and Cellular Endocrinology · doi:10.1016/s0303-7207(02)00157-0 · Cited by 54
LaFleur, G. J., Horiuchi, Y., & Wessel, G. M. (1998) · Mechanisms of Development · doi:10.1016/s0925-4773(97)00178-0 · Cited by 53
Recent Progress and Challenges in CRISPR-Cas9 Engineered Algae and Cyanobacteria
Patel, V. K., Das, A., Kumari, R., & Kajla, S. (2023) · Algal Research · doi:10.1016/j.algal.2023.103068 · Cited by 50
Limited Role for Iron Regulation in Coxiella burnetii Pathogenesis
Briggs, H. L., Pul, N., Seshadri, R., Wilson, M. J., Tersteeg, C., Russell-Lodrigue, K. E., Andoh, M., Bäumler, A. J., & Samuel, J. E. (2008) · Infection and Immunity · doi:10.1128/iai.01609-07 · Cited by 52
Chin, R. M., Panavas, T., Brown, J. M., & Johnson, K. K. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.02.059 · Cited by 50
Kvam, E., & Goldfarb, D. S. (2006) · Journal of Cell Science · doi:10.1242/jcs.03093 · Cited by 47
A no X cel : an Anopheles gambiae protein database
Ribeiro, J. M. C., Topalis, P., & Louis, C. (2004) · Insect Molecular Biology · doi:10.1111/j.0962-1075.2004.00503.x · Cited by 45
Weig, M., Haynes, K., Rogers, T. R., Kurzai, O., Frosch, M., & Mühlschlegel, F. A. (2001) · Microbiology · doi:10.1099/00221287-147-8-2007 · Cited by 46
Identification of four novel ADAMs with potential roles in spermatogenesis and fertilization
Zhu, G.-Z., Lin, Y., Myles, D. G., & Primakoff, P. (1999) · Gene · doi:10.1016/s0378-1119(99)00208-5 · Cited by 45
MORGAN, C. P., INSALL, R., HAYNES, L., & COCKCROFT, S. (2004) · Biochemical Journal · doi:10.1042/bj20040110 · Cited by 35
Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter
Davies, J. S., Currie, M. J., North, R. A., Scalise, M., Wright, J. D., Copping, J. M., Remus, D. M., Gulati, A., Morado, D. R., Jamieson, S. A., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36590-1 · Cited by 34
Selas Castiñeiras, T., Williams, S. G., Hitchcock, A., Cole, J. A., Smith, D. C., & Overton, T. W. (2018) · Scientific Reports · doi:10.1038/s41598-018-25192-3 · Cited by 32
PGA4, a GAS homologue from Candida albicans, is up-regulated early in infection processes
Eckert, S. E., Heinz, W. J., Zakikhany, K., Thewes, S., Haynes, K., Hube, B., & Mühlschlegel, F. A. (2007) · Fungal Genetics and Biology · doi:10.1016/j.fgb.2006.12.006 · Cited by 29
Gonzalez-Fernandez, F., Baer, C. A., & Ghosh, D. (2007) · BMC Biochemistry · doi:10.1186/1471-2091-8-15 · Cited by 23
BRIGÉ, A., COLE, J. A., HAGEN, W. R., GUISEZ, Y., & Van BEEUMEN, J. J. (2001) · Biochemical Journal · doi:10.1042/0264-6021:3560851 · Cited by 23
Zhou, Y.-X., Chen, Y.-X., Tao, X., Cheng, X.-J., & Wang, H.-Y. (2016) · Molecular Genetics and Genomics · doi:10.1007/s00438-015-1134-3 · Cited by 19
Glycoprotein gp130 of Dictyostelium discoideum Influences Macropinocytosis and Adhesion
Chia, C. P., Gomathinayagam, S., Schmaltz, R. J., & Smoyer, L. K. (2005) · Molecular Biology of the Cell · doi:10.1091/mbc.e04-06-0483 · Cited by 11
A computational model for lipid-anchored polysaccharide export by the outer membrane protein GfcD
Fruet, C., Martinez-Goikoetxea, M., Merino, F., & Lupas, A. N. (2024) · Biophysical Journal · doi:10.1016/j.bpj.2024.08.012 · Cited by 1
Metadata
- Authors
- Nielsen, H., Engelbrecht, J., Brunak, S., & von Heijne, G.
- Venue
- Protein Engineering Design and Selection
- Publisher
- Oxford University Press (OUP)
- Published
- 1997-01-01
- Volume
- 10
- Issue
- 1
- Pages
- 1-6
- ISSN
- 0269-2139 (ISSN-L)
- 1741-0126
- 1741-0134
- OpenAlex
- W2171091522
- Cited by
- 5,356
- References
- 0
- FWCI
- 85.50
- Type
- journal article
- Language
- en
- Open access
- bronze
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
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.