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- Käll, Lukas, et al.
(författare)
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A combined transmembrane topology and signal peptide prediction method
- 2004
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 338:5, s. 1027-1036
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Tidskriftsartikel (refereegranskat)abstract
- An inherent problem in transmembrane protein topology prediction and signal peptide prediction is the high similarity between the hydrophobic regions of a transmembrane helix and that of a signal peptide, leading to cross-reaction between the two types of predictions. To improve predictions further, it is therefore important to make a predictor that aims to discriminate between the two classes. In addition, topology information can be gained when successfully predicting a signal Peptide leading a trans' membrane protein since it dictates that the N terminus of the mature protein must be on the non-cytoplasmic side of the membrane. Here, we present Phobius, a combined transmembrane protein topology and signal peptide predictor. The predictor is based on a hidden Markov model (HMM) that models the different sequence regions of a signal peptide and the different regions of a transmembrane protein in a series of interconnected states. Training was done on a newly assembled and curated dataset. Compared to TMHMM and SignalP, errors coming from cross-prediction between transmembrane segments and signal peptides were reduced substantially by Phobius. False classifications of signal peptides were reduced from 26.1% to 3.9% and false classifications of transmembrane helices were reduced from 19.0%, to 7.7%. Phobius was applied to the proteomes of Honzo sapiens and Escherichia coli. Here we also noted a drastic reduction of false classifications compared to TMHMM/SignalP, suggesting that Phobius is well suited for whole-genome annotation of signal peptides and transmembrane regions. The method is available at http://phobius.cgb.ki.se/ as well as at http://phobius.binf.ku.dk/.
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- Käll, Lukas, 1969-, et al.
(författare)
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Reliability of transmembrane predictions in whole-genome data
- 2002
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Ingår i: FEBS Letters. - 0014-5793 .- 1873-3468. ; 532:3, s. 415-418
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Tidskriftsartikel (refereegranskat)abstract
- Transmembrane prediction methods are generally benchmarked on a set of proteins with experimentally verified topology. We have investigated if the accuracy measured on such datasets can be expected in an unbiased genomic analysis, or if there is a bias towards 'easily predictable' proteins in the benchmark datasets. As a measurement of accuracy, the concordance of the results from five different prediction methods was used (TMHMM, PHD, HMMTOP, MEMSAT, and TOPPRED). The benchmark dataset showed significantly higher levels (up to five times) of agreement between different methods than in 10 tested genomes. We have also analyzed which programs are most prone to make mispredictions by measuring the frequency of one-out-of-five disagreeing predictions.
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- Lundin, Carolina, et al.
(författare)
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Membrane topology of the Drosophila OR83b odorant receptor
- 2007
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Ingår i: FEBS Letters. - : Wiley. - 0014-5793 .- 1873-3468. ; 581:29, s. 5601-5604
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Tidskriftsartikel (refereegranskat)abstract
- By analogy to mammals, odorant receptors (ORs) in insects, such as Drosophila melanogaster, have long been thought to belong to the G-protein coupled receptor (GPCR) superfamily. However, recent work has cast doubt on this assumption and has tentatively suggested an inverted topology compared to the canonical N(out) - C(in) 7 transmembrane (TM) GPCR topology, at least for some Drosophila ORs. Here, we report a detailed topology mapping of the Drosophila OR83b receptor using engineered glycosylation sites as topology markers. Our results are inconsistent with a classical GPCR topology and show that OR83b has an intracellular N-terminus, an extracellular C-terminus, and 7TM helices.
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