The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Extensive feature detection of N-terminal protein sorting signals
Open accessAbstract
Motivation: The prediction of localization sites of various proteins is an important and challenging problem in the field of molecular biology. TargetP, by Emanuelsson et al. (J. Mol. Biol. , 300, 1005–1016, 2000) is a neural network based system which is currently the best predictor in the literature for N-terminalsorting signals. One drawback of neural networks, however, is that it is generally difficult to understand and interpret how and why they make such predictions. In this paper, we aim to generate simple and interpretable rules as predictors, and still achieve a practical prediction accuracy. We adopt an approach which consists of an extensive search for simple rules and various attributes which is partially guided by human intuition. Results: We have succeeded in finding rules whose prediction accuracies come close to that of TargetP, while still retaining a very simple and interpretable form. We also discuss and interpret the discovered rules. Availability: An (experimental) web service usingrules obtained by our method is provided at http://hypothesiscreator.net/iPSORT/. Contact: bannai@ims.u-tokyo.ac.jp
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Cites
Comparison of the predicted and observed secondary structure of T4 phage lysozyme
Matthews, B. W. (1975) · Biochimica et Biophysica Acta (BBA) - Protein Structure · doi:10.1016/0005-2795(75)90109-9 · Cited by 5,399 · cited 5×
“The combination of I, u, v, f, w, τ which gives the highest MCC score is recorded.”
MethodInfluentialNakai, K., & Horton, P. (1999) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(98)01336-x · Cited by 2,181 · cited 1×
“PSORT (Nakai and Kanehisa, 1992; Nakai and Horton, 1999) and MitoProt (Claros and Vincens, 1996), unlike TargetP, are systems which incorporate existing knowledge about sorting signals, but they use various real numbers as " weights " in their prediction rules which also may not be trivially…”
BackgroundSelf-citationUsing 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
Cited by
Locating proteins in the cell using TargetP, SignalP and related tools
Emanuelsson, O., Brunak, S., von Heijne, G., & Nielsen, H. (2007) · Nature Protocols · doi:10.1038/nprot.2007.131 · Cited by 3,188
Nelson, B. K., Cai, X., & Nebenführ, A. (2007) · The Plant Journal · doi:10.1111/j.1365-313x.2007.03212.x · Cited by 2,083
Werner, T., Motyka, V., Laucou, V., Smets, R., Van Onckelen, H., & Schmülling, T. (2003) · The Plant Cell · doi:10.1105/tpc.014928 · Cited by 1,527
The Mitochondrial Proteome and Human Disease
Calvo, S. E., & Mootha, V. K. (2010) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082509-141720 · Cited by 590
Liu, T., Song, T., Zhang, X., Yuan, H., Su, L., Li, W., Xu, J., Liu, S., Chen, L., Chen, T., et al. (2014) · Nature Communications · doi:10.1038/ncomms5686 · Cited by 393
Metadata
- Authors
- Bannai, H., Tamada, Y., Maruyama, O., Nakai, K., & Miyano, S.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2002-02-01
- Volume
- 18
- Issue
- 2
- Pages
- 298-305
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2117987251
- Cited by
- 723
- References
- 3
- FWCI
- 13.82
- Type
- journal article
- Language
- en
- Open access
- bronze
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