Improved Prediction of Signal Peptides: SignalP 3.0

McGeoch, 1985, On the predictive recognition of signal peptide sequences, Virus Res., 3, 271, 10.1016/0168-1702(85)90051-6 von Heijne, 1986, A new method for predicting signal sequence cleavage sites, Nucl. Acids Res., 14, 4683, 10.1093/nar/14.11.4683 Nakai, 1991, Expert system for predicting protein localization sites in Gram-negative bacteria, Proteins: Struct. Funct. Genet., 11, 95, 10.1002/prot.340110203 Reinhardt, 1998, Using neural networks for prediction of the subcellular location of proteins, Nucl. Acids Res., 26, 2230, 10.1093/nar/26.9.2230 Hua, 2001, Support vector machine approach for protein subcellular localization prediction, Bioinformatics, 17, 721, 10.1093/bioinformatics/17.8.721 Vert, 2002 Fariselli, 2003, SPEPlip: the detection of signal peptide and lipoprotein cleavage sites, Bioinformatics, 19, 2498, 10.1093/bioinformatics/btg360 Gardy, 2003, PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria, Nucl. Acids Res., 31, 3613, 10.1093/nar/gkg602 Zhang, 2003, A profile hidden Markov model for signal peptides generated by HMMER, Bioinformatics, 19, 307, 10.1093/bioinformatics/19.2.307 Nielsen, 1997, Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites, Protein Eng., 10, 1, 10.1093/protein/10.1.1 Nielsen, 1998, Prediction of signal peptides and signal anchors by a hidden Markov model, Proc. Int. Cong. Intell. Syst. Mol. Biol., 6, 122 Menne, 2000, A comparison of signal sequence prediction methods using a test set of signal peptides, Bioinformatics, 16, 741, 10.1093/bioinformatics/16.8.741 Juncker, 2003, Prediction of lipoprotein signal peptides in Gram-negative bacteria, Protein Sci., 12, 1652, 10.1110/ps.0303703 Nielsen, 1996, Defining a similarity threshold for a functional protein sequence pattern: the signal peptide cleavage site, Proteins: Struct. Funct. Genet., 26, 165, 10.1002/(SICI)1097-0134(199602)24:2<165::AID-PROT4>3.0.CO;2-I Bairoch, 2000, The Swiss-Prot protein sequence database and its supplement TrEMBL in 2000, Nucl. Acids Res., 28, 45, 10.1093/nar/28.1.45 Hobohm, 1992, Selection of representative protein data sets, Protein Sci., 1, 409, 10.1002/pro.5560010313 Karamyshev, 1998, Processing of Escherichia coli alkaline phosphatase: role of the primary structure of the signal peptide cleavage region, J. Mol. Biol., 277, 859, 10.1006/jmbi.1997.1617 Paetzel, 2002, Signal peptidases, Chem. Rev., 102, 4549, 10.1021/cr010166y Lagueux, 1992, Cloning of a Locusta cDNA encoding neuroparsin A, Insect Biochem. Mol. Biol., 22, 511, 10.1016/0965-1748(92)90027-C Palmer, 1990, The primary structure of glycoprotein III from bovine adrenal medullary chromaffin granules. Sequence similarity with human serum protein-40,40 and rat Sertoli cell glycoprotein, J. Biol. Chem., 265, 6617, 10.1016/S0021-9258(19)39193-8 Cedano, 1997, Relation between amino acid composition and cellular location of proteins, J. Mol. Biol., 266, 594, 10.1006/jmbi.1996.0804 Chou, 2001, Prediction of protein cellular attributes using pseudo-amino acid composition, Proteins: Struct. Funct. Genet., 43, 246, 10.1002/prot.1035 Potvin, 1988, Cloning, sequencing and expression of a Bacillus bacteriolytic enzyme in Escherichia coli, Mol. Gen. Genet., 214, 241, 10.1007/BF00337717 Takemaru, 1995, Complete nucleotide sequence of a skin element excised by DNA rearrangement during sporulation in Bacillus subtilis, Microbiology, 141, 323, 10.1099/13500872-141-2-323 Nagaso, 1988, Nucleotide sequence and expression of a Streptomyces griseosporeus proteinaceous alpha-amylase inhibitor (HaimII) gene, J. Bacteriol., 170, 4451, 10.1128/jb.170.10.4451-4457.1988 Aronson, 1989, Gene structure and precursor processing of a novel Bacillus subtilis spore coat protein, Mol. Microbiol., 3, 437, 10.1111/j.1365-2958.1989.tb00189.x Bourne, 1991, Structural and germination defects of Bacillus subtilis spores with altered contents of a spore coat protein, J. Bacteriol., 173, 6618, 10.1128/jb.173.20.6618-6625.1991 Driks, 1999, Bacillus subtilis spore coat, Microbiol. Mol. Biol. Rev., 63, 1, 10.1128/MMBR.63.1.1-20.1999 Driks, 2002, Maximum shields: the assembly and function of the bacterial spore coat, Trends. Microbiol., 10, 251, 10.1016/S0966-842X(02)02373-9 Chada, 2003, Morphogenesis of bacillus spore surfaces, J. Bacteriol., 185, 6255, 10.1128/JB.185.21.6255-6261.2003 Thomas, 2002, Furin at the cutting edge: from protein traffic to embryogenesis and disease, Nature Rev. Mol. Cell Biol., 3, 753, 10.1038/nrm934 Duckert, 2004, Prediction of proprotein convertase cleavage sites, Protein Eng. Des. Sel., 17, 107, 10.1093/protein/gzh013 Nielsen, 1997, A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites, Int. J. Neural Syst., 8, 581, 10.1142/S0129065797000537 Berks, 2000, The Tat protein export pathway, Mol. Microbiol., 35, 260, 10.1046/j.1365-2958.2000.01719.x Palmer, 2003, Moving folded proteins across the bacterial cell membrane, Microbiology, 149, 547, 10.1099/mic.0.25900-0 Miller, 1987, Secretion and processing of staphylococcal nuclease by Bacillus subtilis, J. Bacteriol., 169, 3508, 10.1128/jb.169.8.3508-3514.1987 Kristensen, 1987, cDNA structure of murine C4b-binding protein, a regulatory component of the serum complement system, Biochemistry, 26, 4668, 10.1021/bi00389a012 Horton, 1997, Better prediction of protein cellular localization sites with the k nearest neighbors classifier, Proc. Int. Conf. Intell. Syst. Mol. Biol., 5, 147 Nakai, 1999, PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization, Trends Biochem. Sci., 24, 34, 10.1016/S0968-0004(98)01336-X Krogh, 2001, Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes, J. Mol. Biol., 305, 567, 10.1006/jmbi.2000.4315 Reczko, 2002 Käll, 2004, A combined transmembrane topology and signal peptide prediction method, J. Mol. Biol., 338, 1027, 10.1016/j.jmb.2004.03.016 Bendtsen, 2004, Feature based prediction of non-classical protein secretion, Protein Eng. Des. Sel., 10.1093/protein/gzh037 Mathews, 1975, Comparison of the predicted and observed secondary structure of T4 phage lysozyme, Biochim. Biophys. Acta, 405, 442, 10.1016/0005-2795(75)90109-9