ArticleProtein science : a publication of the Protein Society1996
Topology prediction of membrane proteins.
Article in Protein science : a publication of the Protein Society, 1996. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- The Role of Transmembrane Proteins in Plant Growth, Development, and Stress Responses.International journal of molecular sciences · 2022Review
- Structural analysis of estrogen receptors: interaction between estrogen receptors and cav-1 within the caveolae†.Biology of reproduction · 2019Article
- In silico analysis of Brucella abortus Omp2b and in vitro expression of SOmp2b.Clinical and experimental vaccine research · 2016Article
- Membrane Topology and Biochemical Characterization of the Escherichia coli BacA Undecaprenyl-Pyrophosphate Phosphatase.PloS one · 2015Article
- TOPPER: topology prediction of transmembrane protein based on evidential reasoning.TheScientificWorldJournal · 2013Article
- In silico determination and validation of baumannii acinetobactin utilization a structure and ligand binding site.BioMed research international · 2013Article
- Topological analysis of a haloacid permease of a Burkholderia sp. bacterium with a PhoA-LacZ reporter.BMC microbiology · 2009Article
- Cell surface biliverdin reductase mediates biliverdin-induced anti-inflammatory effects via phosphatidylinositol 3-kinase and Akt.The Journal of biological chemistry · 2009Article
- Comparison of the pseudorabies virus Us9 protein with homologs from other veterinary and human alphaherpesviruses.Journal of virology · 2009Article
- In silico studies on DARC.Infectious disorders drug targets · 2009Review
- Article
- HMM_RA: an improved method for alpha-helical transmembrane protein topology prediction.Bioinformatics and biology insights · 2008Article
- A new approach to the prediction of transmembrane structures.Chinese science bulletin = Kexue tongbao · 2008Article
- Isolation and characterization of a novel haloacid permease from Burkholderia cepacia MBA4.Applied and environmental microbiology · 2007Article
- Article
- A type IV-secretion-like system is required for conjugative DNA transport of broad-host-range plasmid pIP501 in gram-positive bacteria.Journal of bacteriology · 2007Article
- Cleavage map and proteolytic processing of the murine norovirus nonstructural polyprotein in infected cells.Journal of virology · 2006Article
- Asi1 is an inner nuclear membrane protein that restricts promoter access of two latent transcription factors.The Journal of cell biology · 2006Article
- Topology and boundaries of the aerotaxis receptor Aer in the membrane of Escherichia coli.Journal of bacteriology · 2006Article
- Molecular basis for mitochondrial localization of viral particles during beet necrotic yellow vein virus infection.Journal of virology · 2005Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A new method is described for prediction of protein membrane topology (intra- and extracellular sidedness) from multiply aligned amino acid sequences after determination of the membrane-spanning segments. The prediction technique relies on residue compositional differences in the protein segments exposed at each side of the membrane. Intra/extracellular ratios are calculated for the residue types Asn, Asp, Gly, Phe, Pro, Trp, Tyr, and Val, preferably found on the extracellular side, and for Ala, Arg, Cys, and Lys, mostly occurring on the intracellular side. The consensus over these 12 residue distributions is used for sidedness prediction. The method was developed with a test set of 42 protein families, for which all but one were correctly predicted with the new algorithm. This represents an improvement over predictions based on the widely used "positive-inside rule" and other techniques, where at least six mispredictions were observed for the same data set. Further, application of this and other methods to 12 protein families not in the test set still showed the better performance of the present technique, which was subsequently applied to another set of membrane protein families where the topology has yet to be determined.
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