A combined transmembrane topology and signal peptide prediction method.

By Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer. Journal of Molecular Biology, 2004

2,422 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/56bc9dd03848c1d96598897eb10d3ff7dc23836c

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Citations in the corpus

GENCODE: The reference human genome annotation for The ENCODE Project (2012, methodology): “(cid:129) THUMP makes conservative predictions of trans -membrane helices by analyzing the output of three locally installed trans - membrane prediction methods, MemSat (Jones 2007), PRODIV (Viklund and Elofsson 2004), and PHOBIUS (Kall et al. 2004).”
Improving the accuracy of transmembrane protein topology prediction using evolutionary information (2007, methodology): “ Kall et al., 2004 ) where a segment is deemed correctly located if there is at least a 5 residue overlap with the observed segment in the testing set.”
Topology Prediction of α-Helical Transmembrane Proteins (2016, background): “The first version of Phobius [91] was published in 2004.”
Efficient proximity labeling in living cells and organisms with TurboID (2018, neutral): “To calculate specificity, we report the percentage of proteins present in Supplementary Table 2 Tab 4, a list of 11,838 human proteins with secretory annotation according to Phobius 49 , the Human Protein Atlas 50 (protein localized to endoplasmic reticulum, Golgi apparatus, plasma membrane, vesicle”
An HMM posterior decoder for sequence feature prediction that includes homology information (2005, methodology): “We used a recently published HMM, Phobius (Käll et al., 2004), which is a combined transmembrane topology and signal peptide predictor.”
Analysis Tool Web Services from the EMBL-EBI (2013, neutral): “InterProScan (14) and Phobius (15)], etc.”
HMMER web server: 2015 update (2015, methodology): “The protein sequence is also now analysed for the presence of other features: disordered regions using IUPred (15,16), signal peptides and transmembrane regions using Phobius (17) and coiled-coil regions (18).”
Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression (2019, result): “Among these, we defined a consensus set of gold-standard ER-enriched genes as genes identified to be ER-associated by more than 3 of the 5 approaches (Phobius, SignalP, APEX-RIP, proximity-specific ribosome profiling, and MERFISH), resulting in a set of 590 gold-standard ER-enriched genes.”
Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions (2013, methodology): “Transmembrane helices were predicted using Phobius with default parameters (17), coiled-coil regions were predicted using ncoils with default parameters (http://www.”
Prediction of membrane-protein topology from first principles (2008, methodology): “By using the high-resolution benchmark set, SCAMPI and TopPred (cid:1) G were compared against 10 other frequently used topology prediction methods: HMMTOP (4), MEMSAT (26), MEMSAT3 (6), Phobius (17), PolyPhobius (16), PRO-TMHMM (5), PRODIV-TMHMM (5), TMHMM2.”
The in silico human surfaceome (2018, methodology): “The exact borders of all ɑ -helical TM regions were reassessed by using Phobius (7).”