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Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method
Abstract
A new, simple method for predicting transmembrane segments in integral membrane proteins has been developed. It is based on low-stringency dot-plots of the query sequence against a collection of non-homologous membrane proteins using a previously derived scoring matrix [Cserzö et al., 1994, J. Mol. Biol., 243, 388-396]. This so-called dense alignment surface (DAS) method is shown to perform on par with earlier methods that require extra information in the form of multiple sequence alignments or the distribution of positively charged residues outside the transmembrane segments, and thus improves prediction abilities when only single-sequence information is available or for classes of membrane proteins that do not follow the 'positive inside' rule.
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Cited by
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Taylor, B. L., & Zhulin, I. B. (1999) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.63.2.479-506.1999 · Cited by 1,632
Saccone, S. F., Hinrichs, A. L., Saccone, N. L., Chase, G. A., Konvicka, K., Madden, P. A. F., Breslau, N., Johnson, E. O., Hatsukami, D., Pomerleau, O., et al. (2007) · Human Molecular Genetics · doi:10.1093/hmg/ddl438 · Cited by 850
Paszkowski, U., Kroken, S., Roux, C., & Briggs, S. P. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202474599 · Cited by 688
Proteomics of Integral Membrane ProteinsTheory and Application
Speers, A. E., & Wu, C. C. (2007) · Chemical Reviews · doi:10.1021/cr068286z · Cited by 325
Stähler, F. N., Odenbreit, S., Haas, R., Wilrich, J., Vliet, A. H. M. V., Kusters, J. G., Kist, M., & Bereswill, S. (2006) · Infection and Immunity · doi:10.1128/iai.02025-05 · Cited by 148
Metadata
- Authors
- Cserzo, M., Wallin, E., Simon, I., von Heijne, G., & Elofsson, A.
- Venue
- Protein Engineering Design and Selection
- Publisher
- Oxford University Press (OUP)
- Published
- 1997-06-01
- Volume
- 10
- Issue
- 6
- Pages
- 673-676
- ISSN
- 0269-2139 (ISSN-L)
- 1741-0126
- 1741-0134
- OpenAlex
- W2115840790
- Cited by
- 1,034
- References
- 0
- FWCI
- 8.32
- Type
- journal article
- Language
- en
- Open access
- closed
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- CoChat. (2026). Citation check: Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. https://app.cochat.ai/papers/10.1093/protein/10.6.673
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- Cserzo, M., Wallin, E., Simon, I., von Heijne, G., & Elofsson, A. (1997). Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Engineering Design and Selection. https://doi.org/10.1093/protein/10.6.673
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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.
