Improved prediction of signal peptides: SignalP 3.0.

By Jannick Dyrløv Bendtsen, H. Nielsen, G. von Heijne, Søren Brunak. Journal of Molecular Biology, 2004

6,656 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/e7a80ada02b7098645d3e4e5cee9e0093d6b29a5

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Citations in the corpus

ConoServer: updated content, knowledge, and discovery tools in the conopeptide database (2011, methodology): “The ER signal sequence region is identified using the signalP algorithm (32).”
Impacts of bioinformatics to medicinal chemistry. (2015, background): “Many efforts were made in this regard [242-248].”
Molecular Cloning of a β-Galactosidase from Radish That Specifically Hydrolyzes β-(1→3)- and β-(1→6)-Galactosyl Residues of Arabinogalactan Protein1 (2005, methodology): “The cDNA contained a putative signal sequence (30 amino acid residues) preceding the N-terminal sequence of the native enzyme, and this signal sequence agreed well with the prediction by the SignalP program (Bendtsen et al., 2004).”
Widespread Protein Aggregation as an Inherent Part of Aging in C. elegans (2010, neutral): “0 [95], respectively.”
Locating proteins in the cell using TargetP, SignalP and related tools (2007, background): “In version 3, the input to the NN part has been extended by including, in addition to the moving amino-acid windows themselves, the relative position of each window and the overall amino-acid composition of the entire sequenc”
Prediction of the human membrane proteome (2010, methodology): “0 [44] (SignalP), results from prediction methods for membrane protein topology (including SP prediction), and sequence identity to proteins from other genes based on a 50 or 10 amino acid sliding window (HsID 50, HsID 10), are visualized in the protein model.”
Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms (2008, methodology): “If one wishes to predict the signal peptide of a query protein, we would recommend the use of Signal”
FungiDB: an integrated functional genomics database for fungi (2011, methodology): “Genomes and annotation in FungiDB are processed through the same analysis pipeline, which provides additional data, including InterPro domains (26), gene ontology term association (27), signal peptide predictions (28), transmembrane domain predictions, open reading frame predictions, BLAST against t”
Mimicking cellular sorting improves prediction of subcellular localization. (2005, background): “Signal and transit peptides can be recognized by generic prediction methods, that by the detection of these peptides also predict subcellular localization.(17,24,32,33) Many proteins destined for the nucleus contain NLS motifs that may occur anywhere in the sequence.”
Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes (2009, methodology): “Identification of signal peptides at the N-terminus of putative enzymes was performed using the SignalP program [97].”
InterProScan: protein domains identifier (2005, background): “... (Blastall) (4) PRINTS (7) FingerPrintScan (8) SMART (9) Hmmpfam (http://hmmer.wustl.edu/) TIGRFAMs (10) Hmmpfam (http://hmmer.wustl.edu/) Pfam (11) Hmmpfam (http://hmmer.wustl.edu/) PROSITE (12) ScanRegExp + ProfileScan (13) PIRSF (14) Hmmpfam (http://hmmer.wustl.edu/) SUPERFAMILY (15) Hmmpfam (”
Predicting Secretory Proteins with SignalP. (2017, background): “0 from 2004 [17] introduced the D-score for better discrimination between SPs and other sequences and retained the HMM option, while SignalP 4.”
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database (2008, methodology): “Using the standard conﬁguration ﬁle (log4j.properties) the logging can be directed to a ﬁle.”