CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources (original) (raw)

• Rost B, Liu J, Nair R, Wrzeszczynski KO, Ofran Y: Automatic prediction of protein function. Cell Mol Life Sci. 2003, 60 (12): 2637-2650. 10.1007/s00018-003-3114-8.
  Article CAS PubMed Google Scholar
• Nagy A, Hegyi H, Farkas K, Tordai H, Kozma E, Banyai L, Patthy L: Identification and correction of abnormal, incomplete and mispredicted proteins in public databases. BMC bioinformatics. 2008, 9: 353-10.1186/1471-2105-9-353.
  Article PubMed Central PubMed CAS Google Scholar
• Desvaux M, Hebraud M, Talon R, Henderson IR: Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Trends in microbiology. 2009, 17 (4): 139-145. 10.1016/j.tim.2009.01.004.
  Article CAS PubMed Google Scholar
• De-la-Pena C, Lei Z, Watson BS, Sumner LW, Vivanco JM: Root-microbe communication through protein secretion. The Journal of biological chemistry. 2008, 283 (37): 25247-25255. 10.1074/jbc.M801967200.
  Article CAS PubMed Google Scholar
• Steward O, Pollack A, Rao A: Evidence that protein constituents of postsynaptic membrane specializations are locally synthesized: time course of appearance of recently synthesized proteins in synaptic junctions. Journal of neuroscience research. 1991, 30 (4): 649-660. 10.1002/jnr.490300408.
  Article CAS PubMed Google Scholar
• Russo DM, Williams A, Edwards A, Posadas DM, Finnie C, Dankert M, Downie JA, Zorreguieta A: Proteins exported via the PrsD-PrsE type I secretion system and the acidic exopolysaccharide are involved in biofilm formation by Rhizobium leguminosarum. Journal of bacteriology. 2006, 188 (12): 4474-4486. 10.1128/JB.00246-06.
  Article PubMed Central CAS PubMed Google Scholar
• Zhang L, Zhu Z, Jing H, Zhang J, Xiong Y, Yan M, Gao S, Wu LF, Xu J, Kan B: Pleiotropic effects of the twin-arginine translocation system on biofilm formation, colonization, and virulence in Vibrio cholerae. BMC microbiology. 2009, 9: 114-10.1186/1471-2180-9-114.
  Article PubMed Central CAS PubMed Google Scholar
• De Buck E, Anne J, Lammertyn E: The role of protein secretion systems in the virulence of the intracellular pathogen Legionella pneumophila. Microbiology (Reading, England). 2007, 153 (Pt 12): 3948-3953.
  Article CAS Google Scholar
• Poueymiro M, Genin S: Secreted proteins from Ralstonia solanacearum: a hundred tricks to kill a plant. Current opinion in microbiology. 2009, 12 (1): 44-52. 10.1016/j.mib.2008.11.008.
  Article CAS PubMed Google Scholar
• Shrivastava R, Miller JF: Virulence factor secretion and translocation by Bordetella species. Current opinion in microbiology. 2009, 12 (1): 88-93. 10.1016/j.mib.2009.01.001.
  Article PubMed Central CAS PubMed Google Scholar
• Natale P, Bruser T, Driessen AJ: Sec- and Tat-mediated protein secretion across the bacterial cytoplasmic membrane--distinct translocases and mechanisms. Biochimica et biophysica acta. 2008, 1778 (9): 1735-1756. 10.1016/j.bbamem.2007.07.015.
  Article CAS PubMed Google Scholar
• Papanikou E, Karamanou S, Economou A: Bacterial protein secretion through the translocase nanomachine. Nature reviews. 2007, 5 (11): 839-851. 10.1038/nrmicro1771.
  CAS PubMed Google Scholar
• Muller M: Twin-arginine-specific protein export in Escherichia coli. Research in microbiology. 2005, 156 (2): 131-136.
  Article PubMed CAS Google Scholar
• Lee PA, Tullman-Ercek D, Georgiou G: The bacterial twin-arginine translocation pathway. Annual review of microbiology. 2006, 60: 373-395. 10.1146/annurev.micro.60.080805.142212.
  Article PubMed Central PubMed CAS Google Scholar
• Albers SV, Szabo Z, Driessen AJ: Protein secretion in the Archaea: multiple paths towards a unique cell surface. Nature reviews. 2006, 4 (7): 537-547. 10.1038/nrmicro1440.
  CAS PubMed Google Scholar
• Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR: The general secretory pathway: a general misnomer?. Trends in microbiology. 2004, 12 (7): 306-309. 10.1016/j.tim.2004.05.002.
  Article CAS PubMed Google Scholar
• Delepelaire P: Type I secretion in gram-negative bacteria. Biochimica et biophysica acta. 2004, 1694 (1-3): 149-161.
  Article CAS PubMed Google Scholar
• Holland IB, Schmitt L, Young J: Type 1 protein secretion in bacteria, the ABC-transporter dependent pathway (review). Molecular membrane biology. 2005, 22 (1-2): 29-39. 10.1080/09687860500042013.
  Article CAS PubMed Google Scholar
• Galan JE, Wolf-Watz H: Protein delivery into eukaryotic cells by type III secretion machines. Nature. 2006, 444 (7119): 567-573. 10.1038/nature05272.
  Article CAS PubMed Google Scholar
• Ghosh P: Process of protein transport by the type III secretion system. Microbiol Mol Biol Rev. 2004, 68 (4): 771-795. 10.1128/MMBR.68.4.771-795.2004.
  Article PubMed Central CAS PubMed Google Scholar
• Medini D, Covacci A, Donati C: Protein homology network families reveal step-wise diversification of Type III and Type IV secretion systems. PLoS computational biology. 2006, 2 (12): e173-10.1371/journal.pcbi.0020173.
  Article PubMed Central PubMed CAS Google Scholar
• Pukatzki S, McAuley SB, Miyata ST: The type VI secretion system: translocation of effectors and effector-domains. Current opinion in microbiology. 2009, 12 (1): 11-17. 10.1016/j.mib.2008.11.010.
  Article CAS PubMed Google Scholar
• Filloux A, Hachani A, Bleves S: The bacterial type VI secretion machine: yet another player for protein transport across membranes. Microbiology (Reading, England). 2008, 154 (Pt 6): 1570-1583.
  Article CAS Google Scholar
• Desvaux M, Hebraud M, Henderson IR, Pallen MJ: Type III secretion: what's in a name?. Trends in microbiology. 2006, 14 (4): 157-160. 10.1016/j.tim.2006.02.009.
  Article CAS PubMed Google Scholar
• Coulthurst SJ, Palmer T: A new way out: protein localization on the bacterial cell surface via Tat and a novel Type II secretion system. Molecular microbiology. 2008, 69 (6): 1331-1335. 10.1111/j.1365-2958.2008.06367.x.
  Article CAS PubMed Google Scholar
• Cianciotto NP: Type II secretion: a protein secretion system for all seasons. Trends in microbiology. 2005, 13 (12): 581-588. 10.1016/j.tim.2005.09.005.
  Article CAS PubMed Google Scholar
• Mueller CA, Broz P, Cornelis GR: The type III secretion system tip complex and translocon. Molecular microbiology. 2008, 68 (5): 1085-1095. 10.1111/j.1365-2958.2008.06237.x.
  Article CAS PubMed Google Scholar
• Henderson IR, Navarro-Garcia F, Desvaux M, Fernandez RC, Ala'Aldeen D: Type V protein secretion pathway: the autotransporter story. Microbiol Mol Biol Rev. 2004, 68 (4): 692-744. 10.1128/MMBR.68.4.692-744.2004.
  Article PubMed Central CAS PubMed Google Scholar
• Desvaux M, Parham NJ, Henderson IR: Type V protein secretion: simplicity gone awry?. Current issues in molecular biology. 2004, 6 (2): 111-124.
  CAS PubMed Google Scholar
• Nuccio SP, Baumler AJ: Evolution of the chaperone/usher assembly pathway: fimbrial classification goes Greek. Microbiol Mol Biol Rev. 2007, 71 (4): 551-575. 10.1128/MMBR.00014-07.
  Article PubMed Central CAS PubMed Google Scholar
• Sauer FG, Remaut H, Hultgren SJ, Waksman G: Fiber assembly by the chaperone-usher pathway. Biochimica et biophysica acta. 2004, 1694 (1-3): 259-267.
  Article CAS PubMed Google Scholar
• Kostakioti M, Newman CL, Thanassi DG, Stathopoulos C: Mechanisms of protein export across the bacterial outer membrane. Journal of bacteriology. 2005, 187 (13): 4306-4314. 10.1128/JB.187.13.4306-4314.2005.
  Article PubMed Central CAS PubMed Google Scholar
• Bitter W, Houben EN, Luirink J, Appelmelk BJ: Type VII secretion in mycobacteria: classification in line with cell envelope structure. Trends in microbiology. 2009, 17 (8): 337-338. 10.1016/j.tim.2009.05.007.
  Article CAS PubMed Google Scholar
• Desvaux M, Khan A, Scott-Tucker A, Chaudhuri RR, Pallen MJ, Henderson IR: Genomic analysis of the protein secretion systems in Clostridium acetobutylicum ATCC 824. Biochimica et biophysica acta. 2005, 1745 (2): 223-253.
  Article CAS PubMed Google Scholar
• Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP, Saier MH: Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella. Microbiology (Reading, England). 2003, 149 (Pt 11): 3051-3072.
  Article CAS Google Scholar
• Aldridge P, Hughes KT: How and when are substrates selected for type III secretion?. Trends in microbiology. 2001, 9 (5): 209-214. 10.1016/S0966-842X(01)02014-5.
  Article CAS PubMed Google Scholar
• Pallen MJ: The ESAT-6/WXG100 superfamily -- and a new Gram-positive secretion system?. Trends in microbiology. 2002, 10 (5): 209-212. 10.1016/S0966-842X(02)02345-4.
  Article CAS PubMed Google Scholar
• Desvaux M, Hebraud M, Talon R, Henderson IR: Outer membrane translocation: numerical protein secretion nomenclature in question in mycobacteria. Trends in microbiology. 2009, 17 (8): 338-340. 10.1016/j.tim.2009.05.008.
  Article CAS PubMed Google Scholar
• von Heijne G: Patterns of amino acids near signal-sequence cleavage sites. European journal of biochemistry/FEBS. 1983, 133 (1): 17-21. 10.1111/j.1432-1033.1983.tb07424.x.
  Article CAS PubMed Google Scholar
• von Heijne G: A new method for predicting signal sequence cleavage sites. Nucleic acids research. 1986, 14 (11): 4683-4690. 10.1093/nar/14.11.4683.
  Article PubMed Central CAS PubMed Google Scholar
• McGeoch DJ: On the predictive recognition of signal peptide sequences. Virus research. 1985, 3 (3): 271-286. 10.1016/0168-1702(85)90051-6.
  Article CAS PubMed Google Scholar
• Ladunga I, Czako F, Csabai I, Geszti T: Improving signal peptide prediction accuracy by simulated neural network. Comput Appl Biosci. 1991, 7 (4): 485-487.
  CAS PubMed Google Scholar
• Schneider G, Rohlk S, Wrede P: Analysis of cleavage-site patterns in protein precursor sequences with a perceptron-type neural network. Biochemical and biophysical research communications. 1993, 194 (2): 951-959. 10.1006/bbrc.1993.1913.
  Article CAS PubMed Google Scholar
• Plewczynski D, Slabinski L, Ginalski K, Rychlewski L: Prediction of signal peptides in protein sequences by neural networks. Acta biochimica Polonica. 2008, 55 (2): 261-267.
  CAS PubMed Google Scholar
• Nielsen H, Krogh A: Prediction of signal peptides and signal anchors by a hidden Markov model. Proceedings/International Conference on Intelligent Systems for Molecular Biology; ISMB. 1998, 6: 122-130.
  CAS Google Scholar
• Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. Journal of molecular biology. 2004, 340 (4): 783-795. 10.1016/j.jmb.2004.05.028.
  Article PubMed CAS Google Scholar
• Nielsen H, Engelbrecht J, Brunak S, von Heijne G: Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 1997, 10 (1): 1-6. 10.1093/protein/10.1.1.
  Article CAS PubMed Google Scholar
• Kall L, Krogh A, Sonnhammer EL: A combined transmembrane topology and signal peptide prediction method. J Mol Biol. 2004, 338 (5): 1027-1036. 10.1016/j.jmb.2004.03.016.
  Article CAS PubMed Google Scholar
• Kall L, Krogh A, Sonnhammer EL: Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res. 2007, W429-432. 10.1093/nar/gkm256. 35 Web Server
• Zhang Z, Henzel WJ: Signal peptide prediction based on analysis of experimentally verified cleavage sites. Protein Sci. 2004, 13 (10): 2819-2824. 10.1110/ps.04682504.
  Article PubMed Central CAS PubMed Google Scholar
• Berks BC: A common export pathway for proteins binding complex redox cofactors?. Molecular microbiology. 1996, 22 (3): 393-404. 10.1046/j.1365-2958.1996.00114.x.
  Article CAS PubMed Google Scholar
• Rose RW, Bruser T, Kissinger JC, Pohlschroder M: Adaptation of protein secretion to extremely high-salt conditions by extensive use of the twin-arginine translocation pathway. Molecular microbiology. 2002, 45 (4): 943-950. 10.1046/j.1365-2958.2002.03090.x.
  Article CAS PubMed Google Scholar
• Bendtsen JD, Nielsen H, Widdick D, Palmer T, Brunak S: Prediction of twin-arginine signal peptides. BMC Bioinformatics. 2005, 6: 167-10.1186/1471-2105-6-167.
  Article PubMed Central PubMed CAS Google Scholar
• von Heijne G: The structure of signal peptides from bacterial lipoproteins. Protein engineering. 1989, 2 (7): 531-534. 10.1093/protein/2.7.531.
  Article CAS PubMed Google Scholar
• Sankaran K, Gan K, Rash B, Qi HY, Wu HC, Rick PD: Roles of histidine-103 and tyrosine-235 in the function of the prolipoprotein diacylglyceryl transferase of Escherichia coli. Journal of bacteriology. 1997, 179 (9): 2944-2948.
  PubMed Central CAS PubMed Google Scholar
• Berven FS, Karlsen OA, Straume AH, Flikka K, Murrell JC, Fjellbirkeland A, Lillehaug JR, Eidhammer I, Jensen HB: Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools. Archives of microbiology. 2006, 184 (6): 362-377. 10.1007/s00203-005-0055-7.
  Article CAS PubMed Google Scholar
• Babu MM, Priya ML, Selvan AT, Madera M, Gough J, Aravind L, Sankaran K: A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins. Journal of bacteriology. 2006, 188 (8): 2761-2773. 10.1128/JB.188.8.2761-2773.2006.
  Article PubMed Central CAS PubMed Google Scholar
• Bagos PG, Tsirigos KD, Liakopoulos TD, Hamodrakas SJ: Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model. J Proteome Res. 2008, 7 (12): 5082-5093. 10.1021/pr800162c.
  Article CAS PubMed Google Scholar
• Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, Krogh A: Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci. 2003, 12 (8): 1652-1662. 10.1110/ps.0303703.
  Article PubMed Central CAS PubMed Google Scholar
• Klein P, Kanehisa M, DeLisi C: The detection and classification of membrane-spanning proteins. Biochimica et biophysica acta. 1985, 815 (3): 468-476. 10.1016/0005-2736(85)90375-X.
  Article CAS PubMed Google Scholar
• Claros MG, von Heijne G: TopPred II: an improved software for membrane protein structure predictions. Comput Appl Biosci. 1994, 10 (6): 685-686.
  CAS PubMed Google Scholar
• Hirokawa T, Boon-Chieng S, Mitaku S: SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics (Oxford, England). 1998, 14 (4): 378-379. 10.1093/bioinformatics/14.4.378.
  Article CAS Google Scholar
• Jayasinghe S, Hristova K, White SH: Energetics, stability, and prediction of transmembrane helices. Journal of molecular biology. 2001, 312 (5): 927-934. 10.1006/jmbi.2001.5008.
  Article CAS PubMed Google Scholar
• Ganapathiraju M, Jursa CJ, Karimi HA, Klein-Seetharaman J: TMpro web server and web service: transmembrane helix prediction through amino acid property analysis. Bioinformatics. 2007, 23 (20): 2795-2796. 10.1093/bioinformatics/btm398.
  Article PubMed Central CAS PubMed Google Scholar
• Deber CM, Wang C, Liu LP, Prior AS, Agrawal S, Muskat BL, Cuticchia AJ: TM Finder: a prediction program for transmembrane protein segments using a combination of hydrophobicity and nonpolar phase helicity scales. Protein Sci. 2001, 10 (1): 212-219. 10.1110/ps.30301.
  Article PubMed Central CAS PubMed Google Scholar
• Jones DT, Taylor WR, Thornton JM: A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry. 1994, 33 (10): 3038-3049. 10.1021/bi00176a037.
  Article CAS PubMed Google Scholar
• Persson B, Argos P: Prediction of membrane protein topology utilizing multiple sequence alignments. Journal of protein chemistry. 1997, 16 (5): 453-457. 10.1023/A:1026353225758.
  Article CAS PubMed Google Scholar
• Rost B, Fariselli P, Casadio R: Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci. 1996, 5 (8): 1704-1718. 10.1002/pro.5560050824.
  Article PubMed Central CAS PubMed Google Scholar
• Aloy P, Cedano J, Oliva B, Aviles FX, Querol E: 'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins. Comput Appl Biosci. 1997, 13 (3): 231-234.
  CAS PubMed Google Scholar
• Krogh A, Larsson B, von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of molecular biology. 2001, 305 (3): 567-580. 10.1006/jmbi.2000.4315.
  Article CAS PubMed Google Scholar
• Tusnady GE, Simon I: The HMMTOP transmembrane topology prediction server. Bioinformatics. 2001, 17 (9): 849-850. 10.1093/bioinformatics/17.9.849.
  Article CAS PubMed Google Scholar
• Viklund H, Elofsson A: Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci. 2004, 13 (7): 1908-1917. 10.1110/ps.04625404.
  Article PubMed Central CAS PubMed Google Scholar
• Yuan Z, Mattick JS, Teasdale RD: SVMtm: support vector machines to predict transmembrane segments. Journal of computational chemistry. 2004, 25 (5): 632-636. 10.1002/jcc.10411.
  Article CAS PubMed Google Scholar
• Garrow AG, Agnew A, Westhead DR: TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. BMC bioinformatics. 2005, 6: 56-10.1186/1471-2105-6-56.
  Article PubMed Central PubMed CAS Google Scholar
• Garrow AG, Westhead DR: A consensus algorithm to screen genomes for novel families of transmembrane beta barrel proteins. Proteins. 2007, 69 (1): 8-18. 10.1002/prot.21439.
  Article CAS PubMed Google Scholar
• Bagos PG, Liakopoulos TD, Hamodrakas SJ: Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method. BMC bioinformatics. 2005, 6: 7-10.1186/1471-2105-6-7.
  Article PubMed Central PubMed CAS Google Scholar
• Martelli PL, Fariselli P, Krogh A, Casadio R: A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics (Oxford, England). 2002, 18 (Suppl 1): S46-53.
  Article Google Scholar
• Bigelow HR, Petrey DS, Liu J, Przybylski D, Rost B: Predicting transmembrane beta-barrels in proteomes. Nucleic acids research. 2004, 32 (8): 2566-2577. 10.1093/nar/gkh580.
  Article PubMed Central CAS PubMed Google Scholar
• Randall A, Cheng J, Sweredoski M, Baldi P: TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. Bioinformatics (Oxford, England). 2008, 24 (4): 513-520. 10.1093/bioinformatics/btm548.
  Article CAS Google Scholar
• Bigelow H, Rost B: PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Nucleic acids research. 2006, W186-188. 10.1093/nar/gkl262. 34 Web Server
• Hu J, Yan C: A method for discovering transmembrane beta-barrel proteins in Gram-negative bacterial proteomes. Computational biology and chemistry. 2008, 32 (4): 298-301. 10.1016/j.compbiolchem.2008.03.010.
  Article CAS PubMed Google Scholar
• Waldispuhl J, Berger B, Clote P, Steyaert JM: transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. Nucleic acids research. 2006, W189-193. 10.1093/nar/gkl205. 34 Web Server
• Zhai Y, Saier MH: The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes. Protein Sci. 2002, 11 (9): 2196-2207. 10.1110/ps.0209002.
  Article PubMed Central CAS PubMed Google Scholar
• Berven FS, Flikka K, Jensen HB, Eidhammer I: BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria. Nucleic Acids Res. 2004, W394-399. 10.1093/nar/gkh351. 32 Web Server
• Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ: PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins. Nucleic Acids Res. 2004, W400-404. 10.1093/nar/gkh417. 32 Web Server
• Park KJ, Gromiha MM, Horton P, Suwa M: Discrimination of outer membrane proteins using support vector machines. Bioinformatics. 2005, 21 (23): 4223-4229. 10.1093/bioinformatics/bti697.
  Article CAS PubMed Google Scholar
• Ou YY, Gromiha MM, Chen SA, Suwa M: TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles. Computational biology and chemistry. 2008, 32 (3): 227-231. 10.1016/j.compbiolchem.2008.03.002.
  Article CAS PubMed Google Scholar
• Billion A, Ghai R, Chakraborty T, Hain T: Augur--a computational pipeline for whole genome microbial surface protein prediction and classification. Bioinformatics. 2006, 22 (22): 2819-2820. 10.1093/bioinformatics/btl466.
  Article CAS PubMed Google Scholar
• Zhou M, Boekhorst J, Francke C, Siezen RJ: LocateP: genome-scale subcellular-location predictor for bacterial proteins. BMC bioinformatics. 2008, 9: 173-10.1186/1471-2105-9-173.
  Article PubMed Central PubMed CAS Google Scholar
• Choo KH, Tan TW, Ranganathan S: SPdb--a signal peptide database. BMC bioinformatics. 2005, 6: 249-10.1186/1471-2105-6-249.
  Article PubMed Central PubMed CAS Google Scholar
• Rey S, Acab M, Gardy JL, Laird MR, deFays K, Lambert C, Brinkman FS: PSORTdb: a protein subcellular localization database for bacteria. Nucleic Acids Res. 2005, D164-168. 33 Database
• Park S, Yang JS, Jang SK, Kim S: Construction of Functional Interaction Networks through Consensus Localization Predictions of the Human Proteome. J Proteome Res. 2009, 8 (7): 3367-3376. 10.1021/pr900018z.
  Article CAS PubMed Google Scholar
• Restrepo-Montoya D, Vizcaino C, Nino LF, Ocampo M, Patarroyo ME, Patarroyo MA: Validating subcellular localization prediction tools with mycobacterial proteins. BMC Bioinformatics. 2009, 10: 134-10.1186/1471-2105-10-134.
  Article PubMed Central PubMed CAS Google Scholar
• Shen YQ, Burger G: 'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools. BMC Bioinformatics. 2007, 8: 420-10.1186/1471-2105-8-420.
  Article PubMed Central PubMed CAS Google Scholar
• Gupta RS: The natural evolutionary relationships among prokaryotes. Critical reviews in microbiology. 2000, 26 (2): 111-131. 10.1080/10408410091154219.
  Article CAS PubMed Google Scholar
• Rachel R, Wyschkony I, Riehl S, Huber H: The ultrastructure of Ignicoccus: evidence for a novel outer membrane and for intracellular vesicle budding in an archaeon. Archaea (Vancouver, BC). 2002, 1 (1): 9-18. 10.1155/2002/307480.
  Article CAS Google Scholar
• Rudd KE: EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res. 2000, 28 (1): 60-64. 10.1093/nar/28.1.60.
  Article PubMed Central CAS PubMed Google Scholar
• Itoh T, Okayama T, Hashimoto H, Takeda J, Davis RW, Mori H, Gojobori T: A low rate of nucleotide changes in Escherichia coli K-12 estimated from a comparison of the genome sequences between two different substrains. FEBS letters. 1999, 450 (1-2): 72-76. 10.1016/S0014-5793(99)00481-0.
  Article CAS PubMed Google Scholar
• Durfee T, Nelson R, Baldwin S, Plunkett G, Burland V, Mau B, Petrosino JF, Qin X, Muzny DM, Ayele M: The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol. 2008, 190 (7): 2597-2606. 10.1128/JB.01695-07.
  Article PubMed Central CAS PubMed Google Scholar
• Peterson KM, Mekalanos JJ: Characterization of the Vibrio cholerae ToxR regulon: identification of novel genes involved in intestinal colonization. Infection and immunity. 1988, 56 (11): 2822-2829.
  PubMed Central CAS PubMed Google Scholar
• Miyadai H, Tanaka-Masuda K, Matsuyama S, Tokuda H: Effects of lipoprotein overproduction on the induction of DegP (HtrA) involved in quality control in the Escherichia coli periplasm. The Journal of biological chemistry. 2004, 279 (38): 39807-39813. 10.1074/jbc.M406390200.
  Article CAS PubMed Google Scholar
• Thybert D, Avner S, Lucchetti-Miganeh C, Cheron A, Barloy-Hubler F: OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes. BMC genomics. 2008, 9: 637-10.1186/1471-2164-9-637.
  Article PubMed Central PubMed CAS Google Scholar
• Braunstein M, Espinosa BJ, Chan J, Belisle JT, Jacobs WR: SecA2 functions in the secretion of superoxide dismutase A and in the virulence of Mycobacterium tuberculosis. Molecular microbiology. 2003, 48 (2): 453-464. 10.1046/j.1365-2958.2003.03438.x.
  Article CAS PubMed Google Scholar
• Goder V, Spiess M: Topogenesis of membrane proteins: determinants and dynamics. FEBS letters. 2001, 504 (3): 87-93. 10.1016/S0014-5793(01)02712-0.
  Article CAS PubMed Google Scholar
• Martoglio B, Dobberstein B: Signal sequences: more than just greasy peptides. Trends in cell biology. 1998, 8 (10): 410-415. 10.1016/S0962-8924(98)01360-9.
  Article CAS PubMed Google Scholar
• Bingle LE, Bailey CM, Pallen MJ: Type VI secretion: a beginner's guide. Current opinion in microbiology. 2008, 11 (1): 3-8. 10.1016/j.mib.2008.01.006.
  Article CAS PubMed Google Scholar
• Anderson DM, Schneewind O: A mRNA signal for the type III secretion of Yop proteins by Yersinia enterocolitica. Science (New York, NY). 1997, 278 (5340): 1140-1143.
  Article CAS Google Scholar
• Anderson DM, Schneewind O: Yersinia enterocolitica type III secretion: an mRNA signal that couples translation and secretion of YopQ. Molecular microbiology. 1999, 31 (4): 1139-1148. 10.1046/j.1365-2958.1999.01254.x.
  Article CAS PubMed Google Scholar
• Michiels T, Wattiau P, Brasseur R, Ruysschaert JM, Cornelis G: Secretion of Yop proteins by Yersiniae. Infection and immunity. 1990, 58 (9): 2840-2849.
  PubMed Central CAS PubMed Google Scholar
• Lower M, Schneider G: Prediction of type III secretion signals in genomes of gram-negative bacteria. PLoS One. 2009, 4 (6): e5917-10.1371/journal.pone.0005917.
  Article PubMed Central PubMed CAS Google Scholar
• Arnold R, Brandmaier S, Kleine F, Tischler P, Heinz E, Behrens S, Niinikoski A, Mewes HW, Horn M, Rattei T: Sequence-based prediction of type III secreted proteins. PLoS pathogens. 2009, 5 (4): e1000376-10.1371/journal.ppat.1000376.
  Article PubMed Central PubMed CAS Google Scholar
• Hiller K, Grote A, Scheer M, Munch R, Jahn D: PrediSi: prediction of signal peptides and their cleavage positions. Nucleic Acids Res. 2004, W375-379. 10.1093/nar/gkh378. 32 Web Server
• Gomi M, Sonoyama M, Mitaku S: High performance system for signal peptide prediction: SOSUIsignal. Chem-Bio Informatics Journal. 2004, 4 (4): 142-147. 10.1273/cbij.4.142.
  Article CAS Google Scholar
• Mitaku S, Hirokawa T, Tsuji T: Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces. Bioinformatics. 2002, 18 (4): 608-616. 10.1093/bioinformatics/18.4.608.
  Article CAS PubMed Google Scholar
• Juretic D, Zoranic L, Zucic D: Basic charge clusters and predictions of membrane protein topology. J Chem Inf Comput Sci. 2002, 42 (3): 620-632.
  Article CAS PubMed Google Scholar
• Bagos PG, Liakopoulos TD, Hamodrakas SJ: Finding beta-barrel outer membrane proteins with a Markov Chain Model. WSEAS Transactions on Biology and Biomedecine. 2004, 1 (2): 186-189.
  Google Scholar
• Gromiha MM, Ahmad S, Suwa M: TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins. Nucleic Acids Res. 2005, W164-167. 10.1093/nar/gki367. 33 Web Server
• Garrow AG, Agnew A, Westhead DR: TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins. Nucleic Acids Res. 2005, W188-192. 10.1093/nar/gki384. 33 Web Server
• Lu Z, Szafron D, Greiner R, Lu P, Wishart DS, Poulin B, Anvik J, Macdonell C, Eisner R: Predicting subcellular localization of proteins using machine-learned classifiers. Bioinformatics. 2004, 20 (4): 547-556. 10.1093/bioinformatics/btg447.
  Article CAS PubMed Google Scholar
• Matsuda S, Vert JP, Saigo H, Ueda N, Toh H, Akutsu T: A novel representation of protein sequences for prediction of subcellular location using support vector machines. Protein Sci. 2005, 14 (11): 2804-2813. 10.1110/ps.051597405.
  Article PubMed Central CAS PubMed Google Scholar
• Hua S, Sun Z: Support vector machine approach for protein subcellular localization prediction. Bioinformatics. 2001, 17 (8): 721-728. 10.1093/bioinformatics/17.8.721.
  Article CAS PubMed Google Scholar
• Niu B, Jin YH, Feng KY, Lu WC, Cai YD, Li GZ: Using AdaBoost for the prediction of subcellular location of prokaryotic and eukaryotic proteins. Molecular diversity. 2008, 12 (1): 41-45. 10.1007/s11030-008-9073-0.
  Article CAS PubMed Google Scholar
• Imai K, Asakawa N, Tsuji T, Akazawa F, Ino A, Sonoyama M, Mitaku S: SOSUI-GramN: high performance prediction for sub-cellular localization of proteins in Gram-negative bacteria. Bioinformation. 2008, 2 (9): 417-421.
  Article PubMed Central PubMed Google Scholar
• Horler RS, Butcher A, Papangelopoulos N, Ashton PD, Thomas GH: EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations. Bioinformatics. 2009, 25 (2): 163-166. 10.1093/bioinformatics/btn596.
  Article CAS PubMed Google Scholar
• Fernando SA, Selvarani P, Das S, Kumar Ch K, Mondal S, Ramakumar S, Sekar K: THGS: a web-based database of Transmembrane Helices in Genome Sequences. Nucleic Acids Res. 2004, D125-128. 10.1093/nar/gkh130. 32 Database
• Litou ZI, Bagos PG, Tsirigos KD, Liakopoulos TD, Hamodrakas SJ: Prediction of cell wall sorting signals in gram-positive bacteria with a hidden markov model: application to complete genomes. Journal of bioinformatics and computational biology. 2008, 6 (2): 387-401. 10.1142/S0219720008003382.
  Article CAS PubMed Google Scholar
• Remmert M, Linke D, Lupas AN, Soding J: HHomp--prediction and classification of outer membrane proteins. Nucleic Acids Res. 2009, W446-451. 10.1093/nar/gkp325. 37 Web Server
• Saleh MT, Fillon M, Brennan PJ, Belisle JT: Identification of putative exported/secreted proteins in prokaryotic proteomes. Gene. 2001, 269 (1-2): 195-204. 10.1016/S0378-1119(01)00436-X.
  Article CAS PubMed Google Scholar
• Bagos PG, Tsirigos KD, Plessas SK, Liakopoulos TD, Hamodrakas SJ: Prediction of signal peptides in archaea. Protein Eng Des Sel. 2009, 22 (1): 27-35. 10.1093/protein/gzn064.
  Article CAS PubMed Google Scholar
• Ikeda M, Arai M, Okuno T, Shimizu T: TMPDB: a database of experimentally-characterized transmembrane topologies. Nucleic Acids Res. 2003, 31 (1): 406-409. 10.1093/nar/gkg020.
  Article PubMed Central CAS PubMed Google Scholar
• Tusnady GE, Kalmar L, Simon I: TOPDB: topology data bank of transmembrane proteins. Nucleic Acids Res. 2008, D234-239. 36 Database
• Menne KM, Hermjakob H, Apweiler R: A comparison of signal sequence prediction methods using a test set of signal peptides. Bioinformatics. 2000, 16 (8): 741-742. 10.1093/bioinformatics/16.8.741.
  Article CAS PubMed Google Scholar
• Taylor PD, Toseland CP, Attwood TK, Flower DR: LIPPRED: A web server for accurate prediction of lipoprotein signal sequences and cleavage sites. Bioinformation. 2006, 1 (5): 176-179.
  Article PubMed Central PubMed Google Scholar
• Fariselli P, Finocchiaro G, Casadio R: SPEPlip: the detection of signal peptide and lipoprotein cleavage sites. Bioinformatics. 2003, 19 (18): 2498-2499. 10.1093/bioinformatics/btg360.
  Article CAS PubMed Google Scholar
• Bendtsen JD, Kiemer L, Fausboll A, Brunak S: Non-classical protein secretion in bacteria. BMC Microbiol. 2005, 5: 58-10.1186/1471-2180-5-58.
  Article PubMed Central PubMed CAS Google Scholar
• Shen HB, Chou KC: Signal-3L: A 3-layer approach for predicting signal peptides. Biochem Biophys Res Commun. 2007, 363 (2): 297-303. 10.1016/j.bbrc.2007.08.140.
  Article CAS PubMed Google Scholar
• Chou KC, Shen HB: Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides. Biochem Biophys Res Commun. 2007, 357 (3): 633-640. 10.1016/j.bbrc.2007.03.162.
  Article CAS PubMed Google Scholar
• Frank K, Sippl MJ: High-performance signal peptide prediction based on sequence alignment techniques. Bioinformatics. 2008, 24 (19): 2172-2176. 10.1093/bioinformatics/btn422.
  Article CAS PubMed Google Scholar
• Szabo Z, Stahl AO, Albers SV, Kissinger JC, Driessen AJ, Pohlschroder M: Identification of diverse archaeal proteins with class III signal peptides cleaved by distinct archaeal prepilin peptidases. J Bacteriol. 2007, 189 (3): 772-778. 10.1128/JB.01547-06.
  Article PubMed Central CAS PubMed Google Scholar
• Hiss JA, Resch E, Schreiner A, Meissner M, Starzinski-Powitz A, Schneider G: Domain organization of long signal peptides of single-pass integral membrane proteins reveals multiple functional capacity. PLoS One. 2008, 3 (7): e2767-10.1371/journal.pone.0002767.
  Article PubMed Central PubMed CAS Google Scholar
• Reynolds SM, Kall L, Riffle ME, Bilmes JA, Noble WS: Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol. 2008, 4 (11): e1000213-10.1371/journal.pcbi.1000213.
  Article PubMed Central PubMed CAS Google Scholar
• Viklund H, Elofsson A: OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics. 2008, 24 (15): 1662-1668. 10.1093/bioinformatics/btn221.
  Article CAS PubMed Google Scholar
• Viklund H, Bernsel A, Skwark M, Elofsson A: SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinformatics. 2008, 24 (24): 2928-2929. 10.1093/bioinformatics/btn550.
  Article CAS PubMed Google Scholar
• Shen H, Chou JJ: MemBrain: improving the accuracy of predicting transmembrane helices. PLoS One. 2008, 3 (6): e2399-10.1371/journal.pone.0002399.
  Article PubMed Central PubMed CAS Google Scholar
• Cserzo M, Wallin E, Simon I, von Heijne G, Elofsson A: Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Eng. 1997, 10 (6): 673-676. 10.1093/protein/10.6.673.
  Article CAS PubMed Google Scholar
• Bagos PG, Liakopoulos TD, Hamodrakas SJ: Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. BMC Bioinformatics. 2006, 7: 189-10.1186/1471-2105-7-189.
  Article PubMed Central PubMed CAS Google Scholar
• Lo A, Chiu HS, Sung TY, Lyu PC, Hsu WL: Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function. J Proteome Res. 2008, 7 (2): 487-496. 10.1021/pr0702058.
  Article CAS PubMed Google Scholar
• Zhou H, Zhou Y: Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method. Protein Sci. 2003, 12 (7): 1547-1555. 10.1110/ps.0305103.
  Article PubMed Central CAS PubMed Google Scholar
• Pashou EE, Litou ZI, Liakopoulos TD, Hamodrakas SJ: waveTM: wavelet-based transmembrane segment prediction. Silico Biol. 2004, 4 (2): 127-131.
  CAS Google Scholar
• Pasquier C, Promponas VJ, Palaios GA, Hamodrakas JS, Hamodrakas SJ: A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm. Protein Eng. 1999, 12 (5): 381-385. 10.1093/protein/12.5.381.
  Article CAS PubMed Google Scholar
• Peris P, Lopez D, Campos M: IgTM: an algorithm to predict transmembrane domains and topology in proteins. BMC Bioinformatics. 2008, 9: 367-10.1186/1471-2105-9-367.
  Article PubMed Central PubMed CAS Google Scholar
• Bernsel A, Viklund H, Hennerdal A, Elofsson A: TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res. 2009, W465-468. 10.1093/nar/gkp363. 37 Web Server
• Zhou H, Zhang C, Liu S, Zhou Y: Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations. Nucleic Acids Res. 2005, W193-197. 10.1093/nar/gki360. 33 Web Server
• Arai M, Mitsuke H, Ikeda M, Xia JX, Kikuchi T, Satake M, Shimizu T: ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability. Nucleic Acids Res. 2004, W390-393. 10.1093/nar/gkh380. 32 Web Server
• Jones DT: Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics. 2007, 23 (5): 538-544. 10.1093/bioinformatics/btl677.
  Article CAS PubMed Google Scholar
• Adamczak R, Porollo A, Meller J: Combining prediction of secondary structure and solvent accessibility in proteins. Proteins. 2005, 59 (3): 467-475. 10.1002/prot.20441.
  Article PubMed CAS Google Scholar
• Ganapathiraju M, Balakrishnan N, Reddy R, Klein-Seetharaman J: Transmembrane helix prediction using amino acid property features and latent semantic analysis. BMC Bioinformatics. 2008, 9 (Suppl 1): S4-10.1186/1471-2105-9-S1-S4.
  Article PubMed Central PubMed CAS Google Scholar
• Jones DT: Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol. 1999, 292 (2): 195-202. 10.1006/jmbi.1999.3091.
  Article CAS PubMed Google Scholar
• Bryson K, McGuffin LJ, Marsden RL, Ward JJ, Sodhi JS, Jones DT: Protein structure prediction servers at University College London. Nucleic Acids Res. 2005, W36-38. 10.1093/nar/gki410. 33 Web Server
• Combet C, Blanchet C, Geourjon C, Deleage G: NPS@: network protein sequence analysis. Trends Biochem Sci. 2000, 25 (3): 147-150. 10.1016/S0968-0004(99)01540-6.
  Article CAS PubMed Google Scholar
• Karplus K: SAM-T08, HMM-based protein structure prediction. Nucleic Acids Res. 2009, W492-497. 10.1093/nar/gkp403. 37 Web Server
• Pollastri G, McLysaght A: Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics. 2005, 21 (8): 1719-1720. 10.1093/bioinformatics/bti203.
  Article CAS PubMed Google Scholar
• Kahsay RY, Gao G, Liao L: An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes. Bioinformatics. 2005, 21 (9): 1853-1858. 10.1093/bioinformatics/bti303.
  Article CAS PubMed Google Scholar
• Lin K, Simossis VA, Taylor WR, Heringa J: A simple and fast secondary structure prediction method using hidden neural networks. Bioinformatics. 2005, 21 (2): 152-159. 10.1093/bioinformatics/bth487.
  Article CAS PubMed Google Scholar
• Chou KC, Shen HB: MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM. Biochem Biophys Res Commun. 2007, 360 (2): 339-345. 10.1016/j.bbrc.2007.06.027.
  Article CAS PubMed Google Scholar
• Yu CS, Chen YC, Lu CH, Hwang JK: Prediction of protein subcellular localization. Proteins. 2006, 64 (3): 643-651. 10.1002/prot.21018.
  Article CAS PubMed Google Scholar
• Su EC, Chiu HS, Lo A, Hwang JK, Sung TY, Hsu WL: Protein subcellular localization prediction based on compartment-specific features and structure conservation. BMC Bioinformatics. 2007, 8: 330-10.1186/1471-2105-8-330.
  Article PubMed Central PubMed CAS Google Scholar
• Bhasin M, Garg A, Raghava GP: PSLpred: prediction of subcellular localization of bacterial proteins. Bioinformatics. 2005, 21 (10): 2522-2524. 10.1093/bioinformatics/bti309.
  Article CAS PubMed Google Scholar
• Chou KC, Shen HB: Large-scale predictions of gram-negative bacterial protein subcellular locations. J Proteome Res. 2006, 5 (12): 3420-3428. 10.1021/pr060404b.
  Article CAS PubMed Google Scholar
• Shen HB, Chou KC: Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins. Protein Eng Des Sel. 2007, 20 (1): 39-46. 10.1093/protein/gzl053.
  Article CAS PubMed Google Scholar
• Nair R, Rost B: Mimicking cellular sorting improves prediction of subcellular localization. J Mol Biol. 2005, 348 (1): 85-100. 10.1016/j.jmb.2005.02.025.
  Article CAS PubMed Google Scholar
• Jia P, Qian Z, Zeng Z, Cai Y, Li Y: Prediction of subcellular protein localization based on functional domain composition. Biochem Biophys Res Commun. 2007, 357 (2): 366-370. 10.1016/j.bbrc.2007.03.139.
  Article CAS PubMed Google Scholar
• Rashid M, Saha S, Raghava GP: Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs. BMC Bioinformatics. 2007, 8: 337-10.1186/1471-2105-8-337.
  Article PubMed Central PubMed CAS Google Scholar
• Setubal JC, Reis M, Matsunaga J, Haake DA: Lipoprotein computational prediction in spirochaetal genomes. Microbiology. 2006, 152 (Pt 1): 113-121. 10.1099/mic.0.28317-0.
  Article PubMed Central CAS PubMed Google Scholar
• Montgomerie S, Cruz JA, Shrivastava S, Arndt D, Berjanskii M, Wishart DS: PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation. Nucleic Acids Res. 2008, W202-209. 10.1093/nar/gkn255. 36 Web Server
• Pasquier C, Hamodrakas SJ: An hierarchical artificial neural network system for the classification of transmembrane proteins. Protein Eng. 1999, 12 (8): 631-634. 10.1093/protein/12.8.631.
  Article CAS PubMed Google Scholar
• Taylor PD, Attwood TK, Flower DR: BPROMPT: A consensus server for membrane protein prediction. Nucleic Acids Res. 2003, 31 (13): 3698-3700. 10.1093/nar/gkg554.
  Article PubMed Central CAS PubMed Google Scholar
• Liakopoulos TD, Pasquier C, Hamodrakas SJ: A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm. Protein Eng. 2001, 14 (6): 387-390. 10.1093/protein/14.6.387.
  Article CAS PubMed Google Scholar
• Raghava GP: APSSP2: A combination method for protein secondary structure prediction based on neural network and example based learning. CASP5. 2002, A-132:
  Google Scholar
• Simossis VA, Heringa J: PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res. 2005, W289-294. 10.1093/nar/gki390. 33 Web Server
• Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI: OPM: orientations of proteins in membranes database. Bioinformatics. 2006, 22 (5): 623-625. 10.1093/bioinformatics/btk023.
  Article CAS PubMed Google Scholar
• Jayasinghe S, Hristova K, White SH: MPtopo: A database of membrane protein topology. Protein Sci. 2001, 10 (2): 455-458. 10.1110/ps.43501.
  Article PubMed Central CAS PubMed Google Scholar
• Tusnady GE, Dosztanyi Z, Simon I: PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res. 2005, D275-278. 33 Database
• Gromiha MM, Yabuki Y, Kundu S, Suharnan S, Suwa M: TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences. Nucleic Acids Res. 2007, D314-316. 10.1093/nar/gkl805. 35 Database
• Rost B, Yachdav G, Liu J: The PredictProtein server. Nucleic Acids Res. 2004, W321-326. 10.1093/nar/gkh377. 32 Web Server
• Yun H, Lee JW, Jeong J, Chung J, Park JM, Myoung HN, Lee SY: EcoProDB: the Escherichia coli protein database. Bioinformatics. 2007, 23 (18): 2501-2503. 10.1093/bioinformatics/btm351.
  Article CAS PubMed Google Scholar
• Nair R, Rost B: LOCnet and LOCtarget: sub-cellular localization for structural genomics targets. Nucleic Acids Res. 2004, W517-521. 10.1093/nar/gkh441. 32 Web Server
• Zhang S, Xia X, Shen J, Zhou Y, Sun Z: DBMLoc: a Database of proteins with multiple subcellular localizations. BMC Bioinformatics. 2008, 9: 127-10.1186/1471-2105-9-127.
  Article PubMed Central PubMed CAS Google Scholar