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MeSH Review

Databases, Protein

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Disease relevance of Databases, Protein


High impact information on Databases, Protein

  • Dissociation of molecular ions from 9 x 10(-18) mole of carbonic anhydrase gave nine sequence-specific fragment ions, more data than required for unique retrieval of this enzyme from the protein database [6].
  • To test this idea, a protein database search for potential MART-1 epitope mimics was done using criteria developed from analyses of effector recognition of singly-substituted peptide analogues of MART-1(27-35) [7].
  • When tryptic peptides were analyzed by matrix-assisted laser-desorption ionization mass spectrometry and protein database searching, the 40-kilodalton ligand was identified as haptoglobin beta subunit [8].
  • Analysis of protein databases has shown that highly amyloidogenic sequences matching the pattern are less frequent in proteins than innocuous amino acid combinations and that, if present, they are surrounded by amino acids that disrupt their aggregating capability (amyloid breakers) [9].
  • Current knowledge about the determinants of beta-sheet formation has been notably improved by the structural and kinetic analysis of model peptides, by mutagenesis experiments in proteins and by the statistical analysis of the protein structure database (Protein Data Bank; PDB) [10].

Biological context of Databases, Protein

  • Conventional methods of gene prediction rely on the recognition of DNA-sequence signals, the coding potential or the comparison of a genomic sequence with a cDNA, EST, or protein database [11].
  • EBI's Sequence Retrieval System (SRS) is a network browser for databanks in molecular biology, integrating and linking the main nucleotide and protein databases plus many specialised databases [12].
  • Using proteomics technologies, we constructed a two-dimensional protein database for mouse liver, comprising 256 different gene products and investigated the proteins affected after APAP-induced hepatotoxicity [13].
  • MOTIVATION: The SWISS-PROT group at the EBI has developed the Proteome Analysis Database utilizing existing resources and providing comprehensive and integrated comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archaea and eukaryotes [14].
  • A sequence homology search of the SWISSPROT protein sequence data bank with this region from mouse c-Myb has allowed us to identify an area near the C-terminus of repeat 2 that contains a short sequence motif, known as the basic region, which forms the DNA binding site in both leucine zipper and helix-loop-helix transcription factors [15].

Anatomical context of Databases, Protein


Associations of Databases, Protein with chemical compounds


Gene context of Databases, Protein


Analytical, diagnostic and therapeutic context of Databases, Protein


  1. Human single-chain Fv immunoconjugates targeted to a melanoma-associated chondroitin sulfate proteoglycan mediate specific lysis of human melanoma cells by natural killer cells and complement. Wang, B., Chen, Y.B., Ayalon, O., Bender, J., Garen, A. Proc. Natl. Acad. Sci. U.S.A. (1999) [Pubmed]
  2. Purification and cDNA cloning of rat 6-pyruvoyl-tetrahydropterin synthase. Inoue, Y., Kawasaki, Y., Harada, T., Hatakeyama, K., Kagamiyama, H. J. Biol. Chem. (1991) [Pubmed]
  3. A melibiose transporter and an operon containing its gene in Enterobacter cloacae. Okazaki, N., Jue, X.X., Miyake, H., Kuroda, M., Shimamoto, T., Tsuchiya, T. J. Bacteriol. (1997) [Pubmed]
  4. Isolation and sequencing of a gene coding for glyoxalase I activity from Salmonella typhimurium and comparison with other glyoxalase I sequences. Clugston, S.L., Daub, E., Kinach, R., Miedema, D., Barnard, J.F., Honek, J.F. Gene (1997) [Pubmed]
  5. Identification and characterization of the eps (Exopolysaccharide) gene cluster from Streptococcus thermophilus Sfi6. Stingele, F., Neeser, J.R., Mollet, B. J. Bacteriol. (1996) [Pubmed]
  6. Attomole protein characterization by capillary electrophoresis-mass spectrometry. Valaskovic, G.A., Kelleher, N.L., McLafferty, F.W. Science (1996) [Pubmed]
  7. Identification of epitope mimics recognized by CTL reactive to the melanoma/melanocyte-derived peptide MART-1(27-35). Loftus, D.J., Castelli, C., Clay, T.M., Squarcina, P., Marincola, F.M., Nishimura, M.I., Parmiani, G., Appella, E., Rivoltini, L. J. Exp. Med. (1996) [Pubmed]
  8. A circulating ligand for galectin-3 is a haptoglobin-related glycoprotein elevated in individuals with colon cancer. Bresalier, R.S., Byrd, J.C., Tessler, D., Lebel, J., Koomen, J., Hawke, D., Half, E., Liu, K.F., Mazurek, N. Gastroenterology (2004) [Pubmed]
  9. Sequence determinants of amyloid fibril formation. López de la Paz, M., Serrano, L. Proc. Natl. Acad. Sci. U.S.A. (2004) [Pubmed]
  10. The design of linear peptides that fold as monomeric beta-sheet structures. Lacroix, E., Kortemme, T., Lopez de la Paz, M., Serrano, L. Curr. Opin. Struct. Biol. (1999) [Pubmed]
  11. SGP-1: prediction and validation of homologous genes based on sequence alignments. Wiehe, T., Gebauer-Jung, S., Mitchell-Olds, T., Guigó, R. Genome Res. (2001) [Pubmed]
  12. The EMBL nucleotide sequence database. Baker, W., van den Broek, A., Camon, E., Hingamp, P., Sterk, P., Stoesser, G., Tuli, M.A. Nucleic Acids Res. (2000) [Pubmed]
  13. Two-dimensional database of mouse liver proteins: changes in hepatic protein levels following treatment with acetaminophen or its nontoxic regioisomer 3-acetamidophenol. Fountoulakis, M., Berndt, P., Boelsterli, U.A., Crameri, F., Winter, M., Albertini, S., Suter, L. Electrophoresis (2000) [Pubmed]
  14. Interactive InterPro-based comparisons of proteins in whole genomes. Kanapin, A., Apweiler, R., Biswas, M., Fleischmann, W., Karavidopoulou, Y., Kersey, P., Kriventseva, E.V., Mittard, V., Mulder, N., Oinn, T., Phan, I., Servant, F., Zdobnov, E. Bioinformatics (2002) [Pubmed]
  15. The transcriptional control proteins c-Myb and v-Myb contain a basic region DNA binding motif. Carr, M.D., Mott, R.F. FEBS Lett. (1991) [Pubmed]
  16. Stratifin, a keratinocyte specific 14-3-3 protein, harbors a pleckstrin homology (PH) domain and enhances protein kinase C activity. Dellambra, E., Patrone, M., Sparatore, B., Negri, A., Ceciliani, F., Bondanza, S., Molina, F., Cancedda, F.D., De Luca, M. J. Cell. Sci. (1995) [Pubmed]
  17. Proteomic analysis of the human colon carcinoma cell line (LIM 1215): development of a membrane protein database. Simpson, R.J., Connolly, L.M., Eddes, J.S., Pereira, J.J., Moritz, R.L., Reid, G.E. Electrophoresis (2000) [Pubmed]
  18. Interleukin-1beta induced changes in the protein expression of rat islets: a computerized database. Andersen, H.U., Fey, S.J., Larsen, P.M., Nawrocki, A., Hejnaes, K.R., Mandrup-Poulsen, T., Nerup, J. Electrophoresis (1997) [Pubmed]
  19. An on-line two-dimensional polyacrylamide gel electrophoresis protein database of adult Drosophila melanogaster. Ericsson, C., Pethö, Z., Mehlin, H. Electrophoresis (1997) [Pubmed]
  20. An approach to searching protein sequences for superfamily relationships or chance similarities relevant to the molecular mimicry hypothesis: application to the basic proteins of myelin. Weise, M.J., Carnegie, P.R. J. Neurochem. (1988) [Pubmed]
  21. Tnk1: a novel intracellular tyrosine kinase gene isolated from human umbilical cord blood CD34+/Lin-/CD38- stem/progenitor cells. Hoehn, G.T., Stokland, T., Amin, S., Ramírez, M., Hawkins, A.L., Griffin, C.A., Small, D., Civin, C.I. Oncogene (1996) [Pubmed]
  22. Immunochemical characterization of edible bird's nest allergens. Goh, D.L., Chua, K.Y., Chew, F.T., Liang, R.C., Seow, T.K., Ou, K.L., Yi, F.C., Lee, B.W. J. Allergy Clin. Immunol. (2001) [Pubmed]
  23. Characterization and identification of latex allergens by two-dimensional electrophoresis and protein microsequencing. Posch, A., Chen, Z., Wheeler, C., Dunn, M.J., Raulf-Heimsoth, M., Baur, X. J. Allergy Clin. Immunol. (1997) [Pubmed]
  24. Genomically linked cellular protein databases derived from two-dimensional polyacrylamide gel electrophoresis. Neidhardt, F.C., Appleby, D.B., Sankar, P., Hutton, M.E., Phillips, T.A. Electrophoresis (1989) [Pubmed]
  25. BOLD--a biological O-linked glycan database. Cooper, C.A., Wilkins, M.R., Williams, K.L., Packer, N.H. Electrophoresis (1999) [Pubmed]
  26. Changes of voltage-dependent anion-selective channel proteins VDAC1 and VDAC2 brain levels in patients with Alzheimer's disease and Down syndrome. Yoo, B.C., Fountoulakis, M., Cairns, N., Lubec, G. Electrophoresis (2001) [Pubmed]
  27. Evolutionarily conserved ELOVL4 gene expression in the vertebrate retina. Lagali, P.S., Liu, J., Ambasudhan, R., Kakuk, L.E., Bernstein, S.L., Seigel, G.M., Wong, P.W., Ayyagari, R. Invest. Ophthalmol. Vis. Sci. (2003) [Pubmed]
  28. Apisimin, a new serine-valine-rich peptide from honeybee (Apis mellifera L.) royal jelly: purification and molecular characterization. Bíliková, K., Hanes, J., Nordhoff, E., Saenger, W., Klaudiny, J., Simúth, J. FEBS Lett. (2002) [Pubmed]
  29. Cloning and characterization of the human retina-specific gene MPP4, a novel member of the p55 subfamily of MAGUK proteins. Stöhr, H., Weber, B.H. Genomics (2001) [Pubmed]
  30. Probing biomolecular interactions of glutathione transferase M2-2 by using peptide phage display. Edalat, M., Pettersson, S., Persson, M.A., Mannervik, B. Chembiochem (2002) [Pubmed]
  31. The PIR-International Protein Sequence Database. Barker, W.C., Garavelli, J.S., McGarvey, P.B., Marzec, C.R., Orcutt, B.C., Srinivasarao, G.Y., Yeh, L.S., Ledley, R.S., Mewes, H.W., Pfeiffer, F., Tsugita, A., Wu, C. Nucleic Acids Res. (1999) [Pubmed]
  32. Workshop on two-dimensional gel protein databases. Simpson, R.J., Tsugita, A., Celis, J.E., Garrels, J.I., Mewes, H.W. Electrophoresis (1992) [Pubmed]
  33. Electrophoretic analysis of the novel antigen for the gastrointestinal-specific monoclonal antibody, A33. Ji, H., Moritz, R.L., Reid, G.E., Ritter, G., Catimel, B., Nice, E., Heath, J.K., White, S.J., Welt, S., Old, L.J., Burgess, A.W., Simpson, R.J. Electrophoresis (1997) [Pubmed]
  34. IRP1 Ser-711 is a phosphorylation site, critical for regulation of RNA-binding and aconitase activities. Fillebeen, C., Caltagirone, A., Martelli, A., Moulis, J.M., Pantopoulos, K. Biochem. J. (2005) [Pubmed]
  35. The N-glycans of yellow jacket venom hyaluronidases and the protein sequence of its major isoform in Vespula vulgaris. Kolarich, D., Léonard, R., Hemmer, W., Altmann, F. FEBS J. (2005) [Pubmed]
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