Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.

Human non-synonymous SNPs: server and survey. Nucleic Acids Res (2002) 50.45

Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89

SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods (2011) 33.90

GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res (2003) 18.88

SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res (2000) 17.77

The PredictProtein server. Nucleic Acids Res (2004) 10.89

Characterization of VIM-2, a carbapenem-hydrolyzing metallo-beta-lactamase and its plasmid- and integron-borne gene from a Pseudomonas aeruginosa clinical isolate in France. Antimicrob Agents Chemother (2000) 10.05

ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci (1999) 9.82

Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc Natl Acad Sci U S A (2001) 9.40

Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol (2005) 9.13

Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci U S A (2005) 8.52

Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci (1998) 7.88

The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci U S A (2002) 7.21

Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. Nucleic Acids Res (1998) 6.95

Gene expression patterns in human liver cancers. Mol Biol Cell (2002) 6.93

Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci (2003) 6.85

Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14

A stress response pathway from the endoplasmic reticulum to the nucleus requires a novel bifunctional protein kinase/endoribonuclease (Ire1p) in mammalian cells. Genes Dev (1998) 5.88

Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc Natl Acad Sci U S A (2002) 5.28

The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A (2002) 5.28

Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence. Proc Natl Acad Sci U S A (2002) 5.07

Bias of selection on human copy-number variants. PLoS Genet (2006) 4.44

Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs. Proc Natl Acad Sci U S A (1997) 4.40

Nuclear-encoded proteins target to the plastid in Toxoplasma gondii and Plasmodium falciparum. Proc Natl Acad Sci U S A (1998) 4.28

The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res (2002) 4.28

Cloning and characterization of a gene encoding the major surface protein of the bacterial endosymbiont Wolbachia pipientis. J Bacteriol (1998) 4.26

Complete genome sequence of the Q-fever pathogen Coxiella burnetii. Proc Natl Acad Sci U S A (2003) 4.20

Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol (2005) 4.18

ARAMEMNON, a novel database for Arabidopsis integral membrane proteins. Plant Physiol (2003) 4.15

Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. Genome Res (2001) 3.97

The institute for genomic research Osa1 rice genome annotation database. Plant Physiol (2005) 3.96

PrediSi: prediction of signal peptides and their cleavage positions. Nucleic Acids Res (2004) 3.93

Signal peptide-dependent protein transport in Bacillus subtilis: a genome-based survey of the secretome. Microbiol Mol Biol Rev (2000) 3.81

Identification and characterization of the STIM (stromal interaction molecule) gene family: coding for a novel class of transmembrane proteins. Biochem J (2001) 3.77

Can correct protein models be identified? Protein Sci (2003) 3.74

The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol (2001) 3.58

Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol (2008) 3.56

Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet (2011) 3.52

Protein trafficking to the plastid of Plasmodium falciparum is via the secretory pathway. EMBO J (2000) 3.49

A novel CTX-M beta-lactamase (CTX-M-8) in cefotaxime-resistant Enterobacteriaceae isolated in Brazil. Antimicrob Agents Chemother (2000) 3.47

Global analysis of the general stress response of Bacillus subtilis. J Bacteriol (2001) 3.45

The vegetative vacuole proteome of Arabidopsis thaliana reveals predicted and unexpected proteins. Plant Cell (2004) 3.41

Process of protein transport by the type III secretion system. Microbiol Mol Biol Rev (2004) 3.31

Characterization of Saa, a novel autoagglutinating adhesin produced by locus of enterocyte effacement-negative Shiga-toxigenic Escherichia coli strains that are virulent for humans. Infect Immun (2001) 3.29

Shewanella putrefaciens mtrB encodes an outer membrane protein required for Fe(III) and Mn(IV) reduction. J Bacteriol (1998) 3.27

NadA, a novel vaccine candidate of Neisseria meningitidis. J Exp Med (2002) 3.26

NetOglyc: prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glycoconj J (1998) 3.19

The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res (2003) 3.12

Angiopoietin-like proteins stimulate ex vivo expansion of hematopoietic stem cells. Nat Med (2006) 3.09

Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources? BMC Genomics (2009) 3.08

Prediction of twin-arginine signal peptides. BMC Bioinformatics (2005) 3.03

Novel cefotaximase (CTX-M-16) with increased catalytic efficiency due to substitution Asp-240-->Gly. Antimicrob Agents Chemother (2001) 3.03

Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci (2004) 3.02

Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes. Genome Biol (2003) 3.02

The Escherichia coli amidase AmiC is a periplasmic septal ring component exported via the twin-arginine transport pathway. Mol Microbiol (2003) 3.01

OXA-28, an extended-spectrum variant of OXA-10 beta-lactamase from Pseudomonas aeruginosa and its plasmid- and integron-located gene. Antimicrob Agents Chemother (2001) 3.00

FLU: a negative regulator of chlorophyll biosynthesis in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2001) 2.89

Rifins: a second family of clonally variant proteins expressed on the surface of red cells infected with Plasmodium falciparum. Proc Natl Acad Sci U S A (1999) 2.89

Mutations in the fumarate hydratase gene cause hereditary leiomyomatosis and renal cell cancer in families in North America. Am J Hum Genet (2003) 2.88

A bacterial cytokine. Proc Natl Acad Sci U S A (1998) 2.88

Cloning and characterization of two extracellular heparin-degrading endosulfatases in mice and humans. J Biol Chem (2002) 2.86

A comprehensive assessment of N-terminal signal peptides prediction methods. BMC Bioinformatics (2009) 2.85

The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One (2010) 2.84

A new family of potent AB(5) cytotoxins produced by Shiga toxigenic Escherichia coli. J Exp Med (2004) 2.81

IdeS, a novel streptococcal cysteine proteinase with unique specificity for immunoglobulin G. EMBO J (2002) 2.77

Toward a defined anti-Leishmania vaccine targeting vector antigens: characterization of a protective salivary protein. J Exp Med (2001) 2.76

The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. J Bacteriol (2008) 2.71

Use of a whole genome approach to identify vaccine molecules affording protection against Streptococcus pneumoniae infection. Infect Immun (2001) 2.68

The secretory peptide gene EPF1 enforces the stomatal one-cell-spacing rule. Genes Dev (2007) 2.68

Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res (2007) 2.67

A cell-cell signaling peptide activates the PlcR virulence regulon in bacteria of the Bacillus cereus group. EMBO J (2002) 2.66

Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. Plant Cell (2007) 2.66

IBC-1, a novel integron-associated class A beta-lactamase with extended-spectrum properties produced by an Enterobacter cloacae clinical strain. Antimicrob Agents Chemother (2000) 2.62

Inflorescence deficient in abscission controls floral organ abscission in Arabidopsis and identifies a novel family of putative ligands in plants. Plant Cell (2003) 2.62

Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proc Natl Acad Sci U S A (2004) 2.60

Elevated rates of protein secretion, evolution, and disease among tissue-specific genes. Genome Res (2004) 2.58

EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen Phytophthora. Genome Res (2003) 2.57

Identification of a novel neuroligin in humans which binds to PSD-95 and has a widespread expression. Biochem J (2001) 2.55

A pentatricopeptide repeat-containing gene restores fertility to cytoplasmic male-sterile plants. Proc Natl Acad Sci U S A (2002) 2.52

Boosting accuracy of automated classification of fluorescence microscope images for location proteomics. BMC Bioinformatics (2004) 2.46

The murine CAR homolog is a receptor for coxsackie B viruses and adenoviruses. J Virol (1998) 2.45

Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis. Plant Physiol (2003) 2.44

Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo. Nat Struct Mol Biol (2014) 2.43

A novel member of a zinc transporter family is defective in acrodermatitis enteropathica. Am J Hum Genet (2002) 2.41

Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biol (2004) 2.41

Tyrosine cross-linking of extracellular matrix is catalyzed by Duox, a multidomain oxidase/peroxidase with homology to the phagocyte oxidase subunit gp91phox. J Cell Biol (2001) 2.40

Solution structure and dynamics of the outer membrane enzyme PagP by NMR. Proc Natl Acad Sci U S A (2002) 2.39

A modular cloning system for standardized assembly of multigene constructs. PLoS One (2011) 2.39

Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci (2006) 2.39

Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PLoS Biol (2011) 2.38

Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis. PLoS One (2009) 2.38

Sequence conserved for subcellular localization. Protein Sci (2002) 2.36

Detachment of Actinobacillus actinomycetemcomitans biofilm cells by an endogenous beta-hexosaminidase activity. J Bacteriol (2003) 2.32

Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. BMC Genomics (2007) 2.31

Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res (2003) 2.31

Morbilliviruses use signaling lymphocyte activation molecules (CD150) as cellular receptors. J Virol (2001) 2.29

Transmembrane helix predictions revisited. Protein Sci (2002) 2.28

Identification of an apoplastic protein involved in the initial phase of salt stress response in rice root by two-dimensional electrophoresis. Plant Physiol (2008) 2.28

Cloning of the SNG1 gene of Arabidopsis reveals a role for a serine carboxypeptidase-like protein as an acyltransferase in secondary metabolism. Plant Cell (2000) 2.26

Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl Environ Microbiol (2002) 2.24

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol (2001) 66.87

A new method for predicting signal sequence cleavage sites. Nucleic Acids Res (1986) 37.19

Patterns of amino acids near signal-sequence cleavage sites. Eur J Biochem (1983) 26.68

Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol (2000) 22.77

Signal sequences. The limits of variation. J Mol Biol (1985) 21.24

Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J Mol Biol (1999) 15.63

A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol (1998) 14.18

Multiple alignment using simulated annealing: branch point definition in human mRNA splicing. Nucleic Acids Res (1992) 12.08

Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics (2000) 11.75

How signal sequences maintain cleavage specificity. J Mol Biol (1984) 11.03

TopPred II: an improved software for membrane protein structure predictions. Comput Appl Biosci (1994) 10.03

ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci (1999) 9.82

Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Eng (1997) 8.25

Prediction of human mRNA donor and acceptor sites from the DNA sequence. J Mol Biol (1991) 7.93

Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci (1998) 7.88

A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int J Neural Syst (1999) 7.40

Mitochondrial targeting sequences may form amphiphilic helices. EMBO J (1986) 7.11

Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng (1999) 6.72

Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res (1996) 6.13

A DNA structural atlas for Escherichia coli. J Mol Biol (2000) 5.72

Sequence determinants of cytosolic N-terminal protein processing. Eur J Biochem (1986) 5.59

Displaying the information contents of structural RNA alignments: the structure logos. Comput Appl Biosci (1997) 5.51

A conserved cleavage-site motif in chloroplast transit peptides. FEBS Lett (1990) 4.25

Sequence differences between glycosylated and non-glycosylated Asn-X-Thr/Ser acceptor sites: implications for protein engineering. Protein Eng (1990) 4.17

How proteins adapt to a membrane-water interface. Trends Biochem Sci (2000) 3.76

NetOglyc: prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glycoconj J (1998) 3.19

Trans-membrane translocation of proteins. The direct transfer model. Eur J Biochem (1979) 3.13

Determination of the distance between the oligosaccharyltransferase active site and the endoplasmic reticulum membrane. J Biol Chem (1993) 3.02

Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens (2003) 2.93

On the total number of genes and their length distribution in complete microbial genomes. Trends Genet (2001) 2.80

Predicting the topology of eukaryotic membrane proteins. Eur J Biochem (1993) 2.73

YidC, the Escherichia coli homologue of mitochondrial Oxa1p, is a component of the Sec translocase. EMBO J (2000) 2.70

PhosphoBase, a database of phosphorylation sites: release 2.0. Nucleic Acids Res (1999) 2.61

Prediction of human protein function according to Gene Ontology categories. Bioinformatics (2003) 2.54

Membrane proteins: the amino acid composition of membrane-penetrating segments. Eur J Biochem (1981) 2.52

Analysis of the distribution of charged residues in the N-terminal region of signal sequences: implications for protein export in prokaryotic and eukaryotic cells. EMBO J (1984) 2.43

Cleavage-site motifs in mitochondrial targeting peptides. Protein Eng (1990) 2.38

The Escherichia coli SRP and SecB targeting pathways converge at the translocon. EMBO J (1998) 2.35

A receptor component of the chloroplast protein translocation machinery. Science (1994) 2.34

Green fluorescent protein as an indicator to monitor membrane protein overexpression in Escherichia coli. FEBS Lett (2001) 2.28

Fine-tuning the topology of a polytopic membrane protein: role of positively and negatively charged amino acids. Cell (1990) 2.24

env sequences of simian immunodeficiency viruses from chimpanzees in Cameroon are strongly related to those of human immunodeficiency virus group N from the same geographic area. J Virol (2000) 2.17

Cleavage site analysis in picornaviral polyproteins: discovering cellular targets by neural networks. Protein Sci (1996) 2.12

Protein distance constraints predicted by neural networks and probability density functions. Protein Eng (1997) 2.07

Prediction of human protein function from post-translational modifications and localization features. J Mol Biol (2002) 2.05

On the hydrophobic nature of signal sequences. Eur J Biochem (1981) 2.01

Competition between Sec- and TAT-dependent protein translocation in Escherichia coli. EMBO J (1999) 1.95

The biology of eukaryotic promoter prediction--a review. Comput Chem (1999) 1.93

Prediction of organellar targeting signals. Biochim Biophys Acta (2001) 1.93

Structures of N-terminally acetylated proteins. Eur J Biochem (1985) 1.92

Assembly of a cytoplasmic membrane protein in Escherichia coli is dependent on the signal recognition particle. FEBS Lett (1996) 1.89

Topology, subcellular localization, and sequence diversity of the Mlo family in plants. J Biol Chem (1999) 1.88

Nascent membrane and presecretory proteins synthesized in Escherichia coli associate with signal recognition particle and trigger factor. Mol Microbiol (1997) 1.85

Net N-C charge imbalance may be important for signal sequence function in bacteria. J Mol Biol (1986) 1.85

Topological rules for membrane protein assembly in eukaryotic cells. J Biol Chem (1997) 1.83

Amino acid distributions around O-linked glycosylation sites. Biochem J (1991) 1.82

Exploiting the past and the future in protein secondary structure prediction. Bioinformatics (1999) 1.82

O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins. Nucleic Acids Res (1999) 1.81

Prediction of O-glycosylation of mammalian proteins: specificity patterns of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase. Biochem J (1995) 1.81

Anionic phospholipids are determinants of membrane protein topology. EMBO J (1997) 1.77

Molecular mechanism of membrane protein integration into the endoplasmic reticulum. Cell (1997) 1.70

Generating genome-scale candidate gene lists for pharmacogenomics. Clin Pharmacol Ther (2009) 1.66

Prediction of protein secondary structure at 80% accuracy. Proteins (2000) 1.65

Kissing loops hide premature termination codons in pre-mRNA of selenoprotein genes and in genes containing programmed ribosomal frameshifts. RNA (1997) 1.64

Differential use of the signal recognition particle translocase targeting pathway for inner membrane protein assembly in Escherichia coli. Proc Natl Acad Sci U S A (1998) 1.62

Cleaning the GenBank Arabidopsis thaliana data set. Nucleic Acids Res (1996) 1.62

Topological "frustration" in multispanning E. coli inner membrane proteins. Cell (1994) 1.59

G+C-rich tract in 5' end of human introns. J Mol Biol (1992) 1.57

Consensus predictions of membrane protein topology. FEBS Lett (2000) 1.55

Membrane protein topology: effects of delta mu H+ on the translocation of charged residues explain the 'positive inside' rule. EMBO J (1994) 1.53

Statistical analysis of protein kinase specificity determinants. FEBS Lett (1998) 1.53

SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation. Tissue Antigens (2004) 1.52

Translation rate modification by preferential codon usage: intragenic position effects. J Theor Biol (1987) 1.51

A nascent secretory protein may traverse the ribosome/endoplasmic reticulum translocase complex as an extended chain. J Biol Chem (1996) 1.51

Protein secondary structure and homology by neural networks. The alpha-helices in rhodopsin. FEBS Lett (1988) 1.50

The aromatic residues Trp and Phe have different effects on the positioning of a transmembrane helix in the microsomal membrane. Biochemistry (1999) 1.49

DNA structure in human RNA polymerase II promoters. J Mol Biol (1998) 1.46

Towards a comparative anatomy of N-terminal topogenic protein sequences. J Mol Biol (1986) 1.46

Chloroplast transit peptides from the green alga Chlamydomonas reinhardtii share features with both mitochondrial and higher plant chloroplast presequences. FEBS Lett (1990) 1.45

A 30-residue-long "export initiation domain" adjacent to the signal sequence is critical for protein translocation across the inner membrane of Escherichia coli. Proc Natl Acad Sci U S A (1991) 1.43

The distribution of charged amino acids in mitochondrial inner-membrane proteins suggests different modes of membrane integration for nuclearly and mitochondrially encoded proteins. Eur J Biochem (1992) 1.42

Sec dependent and sec independent assembly of E. coli inner membrane proteins: the topological rules depend on chain length. EMBO J (1993) 1.41

Analysis of the secondary structure of the human immunodeficiency virus (HIV) proteins p17, gp120, and gp41 by computer modeling based on neural network methods. J Acquir Immune Defic Syndr (1990) 1.41

Feature-extraction from endopeptidase cleavage sites in mitochondrial targeting peptides. Proteins (1998) 1.41

The 'positive-inside rule' applies to thylakoid membrane proteins. FEBS Lett (1991) 1.40

The COOH-terminal ends of internal signal and signal-anchor sequences are positioned differently in the ER translocase. J Cell Biol (1994) 1.39

Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria. Protein Sci (1997) 1.38

MatrixPlot: visualizing sequence constraints. Bioinformatics (1999) 1.38

Naturally occurring nucleosome positioning signals in human exons and introns. J Mol Biol (1996) 1.38

Genome organisation and chromatin structure in Escherichia coli. Biochimie (2001) 1.37

Determination of the border between the transmembrane and cytoplasmic domains of human integrin subunits. J Biol Chem (1999) 1.37

A turn propensity scale for transmembrane helices. J Mol Biol (1999) 1.37

Signal sequences are not uniformly hydrophobic. J Mol Biol (1982) 1.37

Turns in transmembrane helices: determination of the minimal length of a "helical hairpin" and derivation of a fine-grained turn propensity scale. J Mol Biol (1999) 1.36