Proteome Databases

  • Amos Bairoch
Part of the Principles and Practice book series (PRINCIPLES)

Abstract

The awareness that protein and DNA sequence data are essential to the understanding of biological systems is now well established in the life science community. This community is progressively becoming conscious that this is also true of additional information about protein expression, post-translational modifications, tertiary structure and, of course, function. All of this knowledge needs to be encapsulated in various databases.

Keywords

Maize Lymphoma Codon Mold Cysteine 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Abola EE, Manning NO, Prilusky J, Stampf DR, Sussman JL (1996) The Protein Data Bank: current status and future challenges. J Res Natl Inst Stand Technol 101: 231–241CrossRefGoogle Scholar
  2. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, Kerlavage AR, McCombie WR, Venter JC (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252: 1651–1656PubMedCrossRefGoogle Scholar
  3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410PubMedGoogle Scholar
  4. Anderson NL, Esquer-Blasco R, Hofmann JP, Meheus L, Raymackers J, Steiner S, Witzmann F, Anderson NG (1995) An updated two-dimensional gel database of rat liver proteins useful in gene regulation and drug effects studies. Electrophoresis 16: 1977–1981PubMedCrossRefGoogle Scholar
  5. Antelmann H, Bernhardt J, Schmid R, Mach H, Volker U, Hecker M (1997) First steps from two-dimensional protein index towards a response regulation map for Bacillus subtilis. Electrophoresis 18, in pressGoogle Scholar
  6. Appel RD, Bairoch A, Hochstrasser DF (1994) A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends Biochem Sci 19: 258–260PubMedCrossRefGoogle Scholar
  7. Appel RD, Sanchez JC, Bairoch A, Golaz O, Ravier F, Pasquali C, Hughes GJ, Hochstrasser DF (1996) The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis, its status in 1995. Nucleic Acids Res 24: 180–181PubMedCrossRefGoogle Scholar
  8. Apweiler R, Gateau A, Contrino S, Martin MJ, Junker V, O’Donovan C, Lang F, Mitaritonna N, Kappus S, Bairoch A (1997) Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT + TREMBL. In: ISMB-97; Proceedings 5nd International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo ParkGoogle Scholar
  9. Attwood TK, Beck ME, Bleasby AJ, Degtyarenko K, Michie AD, Parry-Smith DJ (1997) Novel developments with the PRINTS protein fingerprint database. Nucleic Acids Res 25: 212–216PubMedCrossRefGoogle Scholar
  10. Bairoch A (1996) The ENZYME data bank in 1995. Nucleic Acids Res 24: 221–222CrossRefGoogle Scholar
  11. Bairoch A, Apweiler R (1997) The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic Acids Res 25: 31–36PubMedCrossRefGoogle Scholar
  12. Bairoch A, Bucher P, Hofmann K (1997) The PROSITE database, its status in 1997. Nucleic Acids Res 25: 217–221PubMedCrossRefGoogle Scholar
  13. Barry C, Fichant G, Kalogeropoulos A, Quentin Y (1996) A computer filtering method to drive out tiny genes from the yeast genome. Yeast 12: 1163–1178PubMedCrossRefGoogle Scholar
  14. Benson DA, Boguski MS, Lipman DJ, Ostell J (1997) Gen Bank. Nucleic Acids Res 25: 1–6CrossRefGoogle Scholar
  15. Birney E, Thompson JD, Gibson TJ (1996) Pair Wise and Search Wise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. Nucleic Acids Res 24: 2730–2739PubMedCrossRefGoogle Scholar
  16. Blake JA, Richardson JE, Davisson MT, Eppig JT (1997) The Mouse Genome Database (MGD). A comprehensive public resource of genetic, phenotypic and genomic data. Nucleic Acids Res 25: 85–91PubMedCrossRefGoogle Scholar
  17. Bleasby AJ, Akrigg D, Attwood TK (1994) OWL a non-redundant composite protein sequence database. Nucleic Acids Res 22: 3574–3577PubMedGoogle Scholar
  18. Boguski MS, Lowe TMJ, Tolstoshev CM (1993) dbEST-database for expressed sequence tags. Nat Genet 4: 332–333Google Scholar
  19. Borodovsky MY, Koonin EV, Rudd KE (1994) New genes in old sequence: a strategy for finding genes in the bacterial genome. Trends Biochem Sci 19: 309–313PubMedCrossRefGoogle Scholar
  20. Borodovsky MY, Mclninch JD, Koonin EV, Rudd KE, Medigue C, Danchin A (1995) Detection of new genes in a bacterial genome using Markov models for three gene classes. Nucleic Acids Res 23: 3554–3562PubMedCrossRefGoogle Scholar
  21. Boucherie H, Sagliocco F, Joubert R, Maillet I, Labarre J, Perrot M (1996) Two-dimensional gel protein database of Saccharomyces cerevisiae. Electrophoresis 17: 1683–1699PubMedCrossRefGoogle Scholar
  22. Cash P, Argo E, Abadi FJ (1995) Development of a 2-dimensional protein database for Neisseria meningitidis. International Congress of Electrophoresis, ParisGoogle Scholar
  23. Cash P, Argo E, Langford P, Krol SJ (1997) Development of an Haemophilus 2D protein database. Electrophoresis 18, in pressGoogle Scholar
  24. Celis JE, Gromov P, Ostergaard M, Madsen P, Honoré B, Dejgaard K, Olsen E, Vorum H, Kristensen DB, Gromova I, Haunso A, Van Damme J, Puype M, Vandekerckhove J, Rasmussen HH (1996) Human 2-D PAGE databases for proteome analysis in health and disease: http://biobase.dk/cgi-bin/celis. FEBS Lett 398:129–134Google Scholar
  25. Cherry JM, Cartinhour SW, Goodman HM (1992) AAtDB, an Arabidopsis thaliana database. Plant Mol Biol Rep 10: 308–309CrossRefGoogle Scholar
  26. Claverie JM (1993) Detecting frame shifts by amino acid sequence comparison. J Mol Biol 234: 1140–1157PubMedCrossRefGoogle Scholar
  27. Corbett JM, Wheeler CH, Baker CS, Yacoub MH, Dunn MJ (1994) The human myocardial two-dimensional gel protein database: update 1994. Electrophoresis 15: 1459–1465PubMedCrossRefGoogle Scholar
  28. Doolittle RF (1986) Of URFs and ORFs: a primer on how to analyze derived amino acid sequences. University Science Books, Mill Valley, CaliforniaGoogle Scholar
  29. Durbin R, Thierry-Mieg J (1994) The ACEDB genome database. In: Suhai S (ed) Computational methods in genome research. Plenum Press, New York, pp 45–55CrossRefGoogle Scholar
  30. Eddy SR (1996) Hidden Markov models. Curr Opin Struct Biol 6: 361–365PubMedCrossRefGoogle Scholar
  31. Ericsson C, Pethö Z, Mehlin H (1997) An on-line two-dimensional polyacrylamide gel protein database of adult Drosophila melanogaster. Electrophoresis 18: 484–490PubMedCrossRefGoogle Scholar
  32. Fabian P, Murvai J, Hatsagi Z, Vlahovicek K, Hegyi H, Pongor S (1997) The SBASE protein domain library, release 5.0: a collection of annotated protein sequence segments. Nucleic Acids Res 25: 240–243PubMedCrossRefGoogle Scholar
  33. Fasman KH, Letovsky SI, Li P, Cottingham RW, Kingsbury DT (1997) The GDB human genome database Anno 1997. Nucleic Acids Res 25: 72–80PubMedCrossRefGoogle Scholar
  34. FlyBase Consortium (1997) FlyBase: a Drosophila database. Nucleic Acids Res 25: 63–66CrossRefGoogle Scholar
  35. Gevaert K, Verschelde JL, Puype M, Van Damme J, Goethals M, De Boeck S, Vandekerckhove J (1996) Structural analysis and identification of gel-purified proteins, available in the femtomole range, using a novel computer program for peptide sequence assignment, by matrix-assisted laser desorption ionization-reflection time-of-flight-mass spectrometry. Electrophoresis 17: 918–924PubMedCrossRefGoogle Scholar
  36. Giometti CS, Williams K, Tollaksen SL (1997) A two-dimensional electrophoresis database of human breast epithelial cell proteins. Electrophoresis 18: 573–581PubMedCrossRefGoogle Scholar
  37. Guex N, Peitsch MC (1996) Swiss-PdbViewer: a fast and easy-to-use PDB viewer for Macintosh and PC. PDB Quat Newslett 77: 7Google Scholar
  38. Hansen JE, Lund O, Rapacki K, Brunak S (1997) O-GLYCBASE version 2.0: a revised database of 0-glycosylated proteins. Nucleic Acids Res 25: 278–282PubMedCrossRefGoogle Scholar
  39. Henikoff JG, Pietrokovski S, Henikoff S (1997) Recent enhancements to the Blocks database servers. Nucleic Acids Res 25: 222–225PubMedCrossRefGoogle Scholar
  40. Holm L, Sander C (1997) Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res 25: 231–234PubMedCrossRefGoogle Scholar
  41. Jacq B, Horn F, Janody F, Gompel N, Serralbo O, Mohr E, Leroy C, Bellon B, Fasano L, Laurenti P, Röder L (1997) GIF-DB, a WWW database on gene interactions involved in Drosophila melanogaster development. Nucleic Acids Res 25: 67–71PubMedCrossRefGoogle Scholar
  42. James P, Quadroni M, Carafoli E, Gonnet G (1994) Protein identification in DNA databases by peptide mass fingerprinting. Protein Sci 3: 1347–1350PubMedCrossRefGoogle Scholar
  43. Ji H, Reid GE, Moritz RL, Eddes JS, Burgess AW, Simpson RJ (1997) A two-dimensional gel database of human colon carcinoma proteins. Electrophoresis 18: 605–613PubMedCrossRefGoogle Scholar
  44. Jungblut P, Otto A, Zeindl-Eberhardt E, Pleissner KP, Knecht M, Regitz-Zagrosek V, Fleck E, Wittmann-Liebold B (1994) Protein composition of the human heart: the construction of a myocardial two-dimensional electrophoresis database. Electrophoresis 15: 685–707PubMedCrossRefGoogle Scholar
  45. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577–2637PubMedCrossRefGoogle Scholar
  46. Kanehisa M (1996) Toward pathway engineering: a new database of genetic and molecular pathways. Sci Tech Japan 59: 34–38Google Scholar
  47. Karp PD (1997) Metabolic databases. Trends Biochem Sci, in pressGoogle Scholar
  48. Karp PD, Riley M, Paley SM, Pelligrini-Toole A, Krummenacker M (1997) EcoCyc: enyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res 25: 43–50PubMedCrossRefGoogle Scholar
  49. Kolakowski LF Jr (1994) A G-protein-coupled receptor database. Recept Channels 2: 1–7PubMedGoogle Scholar
  50. Kroeger M, Wahl R (1997) Compilation of DNA sequences of Escherichia coli K12: description of the interactive databases ECD and ECDC (update 1996). Nucleic Acids Res 25: 39–42CrossRefGoogle Scholar
  51. Michal G (1982) Biochemical Pathways Wall Chart. Boehringer Mannheim GmbH BiochemicaGoogle Scholar
  52. Moszer I, Glaser P, Danchin A (1995) SubtiList: a relational data base for the Bacillus subtilis genome. Microbiology 141: 261–268PubMedCrossRefGoogle Scholar
  53. NC-IUBMB (1992). Enzyme Nomenclature, Recommendations of the Nomenclature Committe of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes. Academic Press, New-YorkGoogle Scholar
  54. Payne WE, Garrels JI (1997) Yeast Protein Database (YPD): a database for the complete proteome of Saccharomyces cerevisiae. Nucleic Acids Res 25: 57–62PubMedCrossRefGoogle Scholar
  55. Pearson PL, Francomano C, Foster P, Bocchini C, Li P, McKusick VA (1994) The status of online Mendelian inheritance in man (OMIM) medio 1994. Nucleic Acids Res 22: 3470–3473PubMedCrossRefGoogle Scholar
  56. Peitsch MC, Wells TN, Stampf DR, Sussman JL (1995) The Swiss-3Dlmage collection and PDB-Browser on the World-Wide Web. Trends Biochem Sci 20: 82–83PubMedCrossRefGoogle Scholar
  57. Robinson C (1994) The European Bioinformatics Institute (EBI) — open for business. Trends Biotechnol 12: 391–392PubMedCrossRefGoogle Scholar
  58. Rudd KE (1996) Escherichia coli K-12 on the Internet. Trends Genet 12:156–157Google Scholar
  59. Sanchez JC, Appel RD, Golaz O, Pasquali C, Ravier F, Bairoch A, Hochstrasser DF (1995) Inside SWISS-2DPAGE database. Electrophoresis 16: 1131–1151PubMedCrossRefGoogle Scholar
  60. Sayle RA, Milner-White EJ (1995) RASMOL: biomolecular graphics for all. Trends Biochem Sci 19: 258–260Google Scholar
  61. Sazuka T, Ohara O (1997) Towards a proteome project of cyanobacterium Synechocystis sp. strain PCC6803: linking 130 protein spots with their respective genes. Electrophoresis 18, in pressGoogle Scholar
  62. Schneider R, de Davuvar A, Sander C (1997) The HSSP database of protein structure-sequence alignments. Nucleic Acids Res 25: 226–230PubMedCrossRefGoogle Scholar
  63. Selkov E, Galimova M, Goryanin I, Gretchkin Y, Ivanova N, Komarov Y, Maltsev N, Mikhailova N, Nenashev V, Overbeek R, Panyushkina E, Pronevitch L, Selkov E Jr (1997) The metabolic pathway collection: an update. Nucleic Acids Res 25: 37–38PubMedCrossRefGoogle Scholar
  64. Sonnhammer EL, Kahn D (1994) Modular arrangement of proteins as inferred from analysis of homology. Protein Sci 3: 482–492PubMedCrossRefGoogle Scholar
  65. Stoesser G, Sterk P, Tuli MA, Stoehr PJ, Cameron GN (1997) The EMBL Nucleotide Sequence Database. Nucleic Acids Res 25: 7–13PubMedCrossRefGoogle Scholar
  66. Tateno Y, Gojobori T (1997) DNA Data Bank of Japan in the age of information biology. Nucleic Acids Res 25: 14–17PubMedCrossRefGoogle Scholar
  67. VanBogelen RA, Abshire KZ, Pertsemlidis A, Clark RL, Neidhardt FC (1996) Gene-protein database of Escherichia coli K-12, edition 6. In: Neidhardt FC (ed) Escherichia coli and Salmonella typhimurium: cellular and molecular biology, 2nd edn. ASM Press, Washington DC, pp 2067–2117Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1997

Authors and Affiliations

  • Amos Bairoch

There are no affiliations available

Personalised recommendations