Predicting transmembrane beta-barrels in proteomes.

Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput Biol (2006) 2.15

Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development. J Biomed Biotechnol (2010) 1.55

A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinformatics (2005) 1.49

Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method. BMC Bioinformatics (2005) 1.41

Protein secretion and outer membrane assembly in Alphaproteobacteria. FEMS Microbiol Rev (2008) 1.37

Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays. Infect Immun (2009) 1.30

An outer membrane receptor of Neisseria meningitidis involved in zinc acquisition with vaccine potential. PLoS Pathog (2010) 1.19

Membrane protein prediction methods. Methods (2007) 1.17

HHomp--prediction and classification of outer membrane proteins. Nucleic Acids Res (2009) 1.16

Structural genomics target selection for the New York consortium on membrane protein structure. J Struct Funct Genomics (2009) 1.14

Emerging vaccine informatics. J Biomed Biotechnol (2011) 1.12

TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins. Nucleic Acids Res (2005) 1.10

The chloroplast protein translocation complexes of Chlamydomonas reinhardtii: a bioinformatic comparison of Toc and Tic components in plants, green algae and red algae. Genetics (2008) 1.09

Verification of a topology model of PorT as an integral outer-membrane protein in Porphyromonas gingivalis. Microbiology (2009) 1.09

TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins. Nucleic Acids Res (2005) 1.06

OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria. Nucleic Acids Res (2010) 1.04

Trimeric structure of major outer membrane proteins homologous to OmpA in Porphyromonas gingivalis. J Bacteriol (2005) 1.04

TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. BMC Bioinformatics (2005) 1.03

PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res (2006) 1.01

New Escherichia coli outer membrane proteins identified through prediction and experimental verification. Protein Sci (2006) 1.00

Simultaneous prediction of protein secondary structure and transmembrane spans. Proteins (2013) 1.00

An automatic method for identifying surface proteins in bacteria: SLEP. BMC Bioinformatics (2010) 0.96

Characterization and comparative analysis of the genes encoding Haemophilus parasuis outer membrane proteins P2 and P5. J Bacteriol (2009) 0.95

Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome. FEMS Microbiol Rev (2008) 0.90

CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources. BMC Microbiol (2010) 0.90

Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism. Acta Crystallogr Sect F Struct Biol Cryst Commun (2009) 0.89

TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences. Nucleic Acids Res (2006) 0.89

Comparative analysis of the biochemical and functional properties of C-terminal domains of autotransporters. J Bacteriol (2010) 0.88

Pattern of amino acid substitutions in transmembrane domains of β-barrel membrane proteins for detecting remote homologs in bacteria and mitochondria. PLoS One (2011) 0.87

Detecting remote homologues using scoring matrices calculated from the estimation of amino acid substitution rates of beta-barrel membrane proteins. Conf Proc IEEE Eng Med Biol Soc (2008) 0.86

Is the C-terminal insertional signal in Gram-negative bacterial outer membrane proteins species-specific or not? BMC Genomics (2012) 0.86

Prediction of beta-barrel membrane proteins by searching for restricted domains. BMC Bioinformatics (2005) 0.84

transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. Nucleic Acids Res (2006) 0.83

TMBB-DB: a transmembrane β-barrel proteome database. Bioinformatics (2012) 0.81

Ferric-pyoverdine recognition by Fpv outer membrane proteins of Pseudomonas protegens Pf-5. J Bacteriol (2012) 0.80

Outer membrane proteins can be simply identified using secondary structure element alignment. BMC Bioinformatics (2011) 0.79

Mutational analyses reveal overall topology and functional regions of NilB, a bacterial outer membrane protein required for host association in a model of animal-microbe mutualism. J Bacteriol (2012) 0.79

Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications. Algorithms Mol Biol (2009) 0.78

The C-terminus of Bienertia sinuspersici Toc159 contains essential elements for its targeting and anchorage to the chloroplast outer membrane. Front Plant Sci (2014) 0.77

A graph-theoretic approach for classification and structure prediction of transmembrane β-barrel proteins. BMC Genomics (2012) 0.77

Improved prediction of trans-membrane spans in proteins using an Artificial Neural Network. IEEE Symp Comput Intell Bioinforma Comput Biol Proc (2009) 0.77

Mosaic composition of ribA and wspB genes flanking the virB8-D4 operon in the Wolbachia supergroup B-strain, wStr. Arch Microbiol (2015) 0.76

Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC). BMC Genomics (2016) 0.76

Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting. BMC Evol Biol (2015) 0.75

TMSEG: Novel prediction of transmembrane helices. Proteins (2016) 0.75

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase. Comput Struct Biotechnol J (2017) 0.75

Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters. Microb Cell Fact (2016) 0.75

Genome Report: Identification and Validation of Antigenic Proteins from Pajaroellobacter abortibovis Using De Novo Genome Sequence Assembly and Reverse Vaccinology. G3 (Bethesda) (2016) 0.75

The Protein Data Bank. Nucleic Acids Res (2000) 187.10

A simple method for displaying the hydropathic character of a protein. J Mol Biol (1982) 150.65

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69

The complete genome sequence of Escherichia coli K-12. Science (1997) 84.27

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res (2000) 67.44

Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins (1991) 32.50

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res (2001) 22.33

Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta (1975) 17.03

Membrane protein folding and stability: physical principles. Annu Rev Biophys Biomol Struct (1999) 10.13

Twilight zone of protein sequence alignments. Protein Eng (1999) 9.83

Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature (2002) 8.42

Genome sequence of Yersinia pestis KIM. J Bacteriol (2002) 7.14

Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol (2002) 6.96

Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae. Lancet (2003) 6.95

Siderophore-mediated iron transport: crystal structure of FhuA with bound lipopolysaccharide. Science (1998) 5.62

Crystal structure of the outer membrane active transporter FepA from Escherichia coli. Nat Struct Biol (1999) 4.86

Structure and function of bacterial outer membrane proteins: barrels in a nutshell. Mol Microbiol (2000) 4.59

Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83. J Bacteriol (2003) 4.41

Review: protein secondary structure prediction continues to rise. J Struct Biol (2001) 3.91

GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. Methods Enzymol (2003) 3.58

Transmembrane signaling across the ligand-gated FhuA receptor: crystal structures of free and ferrichrome-bound states reveal allosteric changes. Cell (1998) 3.27

The versatile beta-barrel membrane protein. Curr Opin Struct Biol (2003) 2.82

The PredictProtein server. Nucleic Acids Res (2003) 2.72

The structure of a mycobacterial outer-membrane channel. Science (2004) 2.56

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

The HSSP database of protein structure-sequence alignments. Nucleic Acids Res (1997) 2.44

High-resolution structure of the OmpA membrane domain. J Mol Biol (2000) 2.40

Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose. Nat Struct Biol (1998) 2.39

EVA: large-scale analysis of secondary structure prediction. Proteins (2001) 2.38

The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence. Structure (1999) 2.36

A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment. Proteins (1999) 2.35

Wanted: subcellular localization of proteins based on sequence. Trends Cell Biol (1998) 2.30

Transmembrane helix predictions revisited. Protein Sci (2002) 2.28

Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures. Protein Sci (2002) 2.25

Crystal structure of the outer membrane protease OmpT from Escherichia coli suggests a novel catalytic site. EMBO J (2001) 2.24

A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics (2002) 2.23

beta-Barrel membrane proteins. Curr Opin Struct Biol (2000) 2.20

Structural evidence for dimerization-regulated activation of an integral membrane phospholipase. Nature (1999) 2.07

Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies. In Silico Biol (2002) 2.07

Mycobacterial porins--new channel proteins in unique outer membranes. Mol Microbiol (2003) 2.04

Refined structure of the porin from Rhodopseudomonas blastica. Comparison with the porin from Rhodobacter capsulatus. J Mol Biol (1994) 1.89

Redefining the goals of protein secondary structure prediction. J Mol Biol (1994) 1.84

UniqueProt: Creating representative protein sequence sets. Nucleic Acids Res (2003) 1.78

Molecular design of PhoE porin and its functional consequences. J Mol Biol (1989) 1.50

Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor. Protein Sci (2001) 1.49

Structure of maltoporin from Salmonella typhimurium ligated with a nitrophenyl-maltotrioside. J Mol Biol (1997) 1.45

PEP: Predictions for Entire Proteomes. Nucleic Acids Res (2003) 1.39

The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes. Protein Sci (2002) 1.38

Channel specificity: structural basis for sugar discrimination and differential flux rates in maltoporin. J Mol Biol (1997) 1.33

Stability of trimeric OmpF porin: the contributions of the latching loop L2. Biochemistry (1998) 1.32

Biochemical and biophysical characterization of OmpG: A monomeric porin. Biochemistry (2000) 1.32

Prediction of the plant beta-barrel proteome: a case study of the chloroplast outer envelope. Protein Sci (2003) 1.30

Prediction by a neural network of outer membrane beta-strand protein topology. Protein Sci (1998) 1.29

A tetrameric porin limits the cell wall permeability of Mycobacterium smegmatis. J Biol Chem (2002) 1.23

The preprotein conducting channel at the inner envelope membrane of plastids. EMBO J (2002) 1.22

CHOP proteins into structural domain-like fragments. Proteins (2004) 1.21

A HMM-based method to predict the transmembrane regions of beta-barrel membrane proteins. Comput Biol Chem (2003) 1.18

Structure and dynamics of the beta-barrel of the membrane transporter BtuB by site-directed spin labeling. Biochemistry (2002) 1.18

Voltage sensing in the PhoE and OmpF outer membrane porins of Escherichia coli: role of charged residues. J Mol Biol (1997) 1.17

Bacterial phospholipase A: structure and function of an integral membrane phospholipase. Biochim Biophys Acta (2000) 1.13

Type I secretion and multidrug efflux: transport through the TolC channel-tunnel. Trends Biochem Sci (2001) 1.13

Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries. Bioinformatics (1999) 1.12

Pore functioning of outer membrane protein PhoE of Escherichia coli: mutagenesis of the constriction loop L3. Protein Eng (1997) 1.12

Principles of membrane protein assembly and structure. Prog Biophys Mol Biol (1996) 1.11

State-of-the-art in membrane protein prediction. Appl Bioinformatics (2002) 1.11

Identification of membrane spanning beta strands in bacterial porins. Protein Eng (1997) 1.00

MOMP, a divergent porin from Campylobacter: cloning and primary structural characterization. Biochem Biophys Res Commun (2001) 0.98

Structure of PhoE porin in projection at 3.5 A resolution. J Struct Biol (1990) 0.97

Review: prediction of in vivo fates of proteins in the era of genomics and proteomics. J Struct Biol (2001) 0.94

Structural investigations of calcium binding and its role in activity and activation of outer membrane phospholipase A from Escherichia coli. J Mol Biol (2001) 0.88

Insertion mutagenesis and membrane topology model of the Pseudomonas aeruginosa outer membrane protein OprM. J Bacteriol (2000) 0.86

Predicting protein conformation by statistical methods. Biochim Biophys Acta (2001) 0.80

High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97

SNAP predicts effect of mutations on protein function. Bioinformatics (2008) 15.39

The PredictProtein server. Nucleic Acids Res (2004) 10.89

The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature (2010) 10.04

Non-canonical inflammasome activation targets caspase-11. Nature (2011) 8.85

SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res (2007) 8.46

Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol (2009) 6.76

Sensitivity to antitubulin chemotherapeutics is regulated by MCL1 and FBW7. Nature (2011) 5.32

Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins (2002) 5.29

A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61

The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res (2002) 4.58

A mutation in VPS35, encoding a subunit of the retromer complex, causes late-onset Parkinson disease. Am J Hum Genet (2011) 4.52

Deubiquitinase USP9X stabilizes MCL1 and promotes tumour cell survival. Nature (2009) 4.12

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11

Finished bacterial genomes from shotgun sequence data. Genome Res (2012) 3.86

Critical assessment of methods of protein structure prediction-Round VII. Proteins (2007) 3.23

Mimicking cellular sorting improves prediction of subcellular localization. J Mol Biol (2005) 3.21

Three-dimensional structures of membrane proteins from genomic sequencing. Cell (2012) 3.02

Analysing six types of protein-protein interfaces. J Mol Biol (2003) 2.96

The African coelacanth genome provides insights into tetrapod evolution. Nature (2013) 2.78

The PredictProtein server. Nucleic Acids Res (2003) 2.72

Loss of the tumor suppressor BAP1 causes myeloid transformation. Science (2012) 2.69

Critical assessment of methods of protein structure prediction (CASP)--round 6. Proteins (2005) 2.58

Alignments grow, secondary structure prediction improves. Proteins (2002) 2.56

USP1 deubiquitinates ID proteins to preserve a mesenchymal stem cell program in osteosarcoma. Cell (2011) 2.51

EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res (2003) 2.50

Reliability of assessment of protein structure prediction methods. Structure (2002) 2.39

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

Automatic target selection for structural genomics on eukaryotes. Proteins (2004) 2.34

Outcome of a workshop on archiving structural models of biological macromolecules. Structure (2006) 2.32

The protein target list of the Northeast Structural Genomics Consortium. Proteins (2004) 2.31

Transmembrane helix predictions revisited. Protein Sci (2002) 2.28

Association of C-terminal ubiquitin hydrolase BRCA1-associated protein 1 with cell cycle regulator host cell factor 1. Mol Cell Biol (2009) 2.26

Critical assessment of methods of protein structure prediction - Round VIII. Proteins (2009) 2.25

The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Res (2012) 2.19

Protein-protein interaction hotspots carved into sequences. PLoS Comput Biol (2007) 2.15

PROFbval: predict flexible and rigid residues in proteins. Bioinformatics (2006) 2.04

Domains, motifs and clusters in the protein universe. Curr Opin Chem Biol (2003) 2.02

Predicted protein-protein interaction sites from local sequence information. FEBS Lett (2003) 2.00

Loopy proteins appear conserved in evolution. J Mol Biol (2002) 1.96

PSI-2: structural genomics to cover protein domain family space. Structure (2009) 1.92

Deubiquitinase USP37 is activated by CDK2 to antagonize APC(CDH1) and promote S phase entry. Mol Cell (2011) 1.92

Phosphorylation of NLRC4 is critical for inflammasome activation. Nature (2012) 1.92

Protein names precisely peeled off free text. Bioinformatics (2004) 1.87

COP1 is a tumour suppressor that causes degradation of ETS transcription factors. Nature (2011) 1.83

Distinguishing protein-coding from non-coding RNAs through support vector machines. PLoS Genet (2006) 1.81

NLSdb: database of nuclear localization signals. Nucleic Acids Res (2003) 1.81

PROFcon: novel prediction of long-range contacts. Bioinformatics (2005) 1.81

UniqueProt: Creating representative protein sequence sets. Nucleic Acids Res (2003) 1.78

Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data. Nat Biotechnol (2009) 1.78

Effects of permissive hypercapnia on transient global cerebral ischemia-reperfusion injury in rats. Anesthesiology (2010) 1.78

Comprehensive in silico mutagenesis highlights functionally important residues in proteins. Bioinformatics (2008) 1.74

Prediction of DNA-binding residues from sequence. Bioinformatics (2007) 1.72

ISIS: interaction sites identified from sequence. Bioinformatics (2007) 1.71

Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo. J Exp Med (2013) 1.71

Epitome: database of structure-inferred antigenic epitopes. Nucleic Acids Res (2006) 1.70

Improved disorder prediction by combination of orthogonal approaches. PLoS One (2009) 1.63

Continuum secondary structure captures protein flexibility. Structure (2002) 1.63

Better prediction of sub-cellular localization by combining evolutionary and structural information. Proteins (2003) 1.61

Protein-protein interactions more conserved within species than across species. PLoS Comput Biol (2006) 1.61

Protein flexibility and rigidity predicted from sequence. Proteins (2005) 1.58

NORSp: Predictions of long regions without regular secondary structure. Nucleic Acids Res (2003) 1.58

Novel leverage of structural genomics. Nat Biotechnol (2007) 1.57

Inferring sub-cellular localization through automated lexical analysis. Bioinformatics (2002) 1.55

Structural genomics is the largest contributor of novel structural leverage. J Struct Funct Genomics (2009) 1.52

Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery. Drug Discov Today (2005) 1.46

Natively unstructured regions in proteins identified from contact predictions. Bioinformatics (2007) 1.45

PEP: Predictions for Entire Proteomes. Nucleic Acids Res (2003) 1.39

CASP6 assessment of contact prediction. Proteins (2005) 1.39

Protein disorder--a breakthrough invention of evolution? Curr Opin Struct Biol (2011) 1.37

Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins (2006) 1.35

Target space for structural genomics revisited. Bioinformatics (2002) 1.32

Microphthalmia-associated transcription factor is a critical transcriptional regulator of melanoma inhibitor of apoptosis in melanomas. Cancer Res (2008) 1.28

Solution NMR structure of the NlpC/P60 domain of lipoprotein Spr from Escherichia coli: structural evidence for a novel cysteine peptidase catalytic triad. Biochemistry (2008) 1.27

Crystal structure of a potassium ion transporter, TrkH. Nature (2011) 1.25

Homologue structure of the SLAC1 anion channel for closing stomata in leaves. Nature (2010) 1.22

Sequence-based prediction of protein domains. Nucleic Acids Res (2004) 1.21

CHOP proteins into structural domain-like fragments. Proteins (2004) 1.21

DSSPcont: Continuous secondary structure assignments for proteins. Nucleic Acids Res (2003) 1.20

Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination. J Am Chem Soc (2005) 1.19

Natively unstructured loops differ from other loops. PLoS Comput Biol (2007) 1.19

LOC3D: annotate sub-cellular localization for protein structures. Nucleic Acids Res (2003) 1.18

Membrane protein prediction methods. Methods (2007) 1.17

SNPdbe: constructing an nsSNP functional impacts database. Bioinformatics (2011) 1.16

Better prediction of functional effects for sequence variants. BMC Genomics (2015) 1.16

MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence. Bioinformatics (2008) 1.15

Structural genomics target selection for the New York consortium on membrane protein structure. J Struct Funct Genomics (2009) 1.14

LOCnet and LOCtarget: sub-cellular localization for structural genomics targets. Nucleic Acids Res (2004) 1.12

LocTree2 predicts localization for all domains of life. Bioinformatics (2012) 1.11

State-of-the-art in membrane protein prediction. Appl Bioinformatics (2002) 1.11