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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review


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Disease relevance of Databases

  • Amino acid residues 28 to 112 of the deduced MRP7 sequence aligned with the 84 residues of the Escherichia coli ribosomal protein L27, but no significant similarity was detected between the carboxy-terminal 259 amino acids of MRP7 and other protein sequences in existing computer data bases [1].
  • We have determined the x-ray crystal structure of a beta-hexosaminidase from Streptomyces plicatus to 2.2 A resolution (Protein Data Bank code ). beta-Hexosaminidases are believed to use a substrate-assisted catalytic mechanism that generates a cyclic oxazolinium ion intermediate [2].
  • OBJECTIVES: The purpose of this Asymptomatic Cardiac Ischemia Pilot (ACIP) data bank study was to characterize angiographic features of coronary pathology of patients enrolled in the ACIP study [3].
  • This report describes the construction and the anti-human immunodeficiency virus type 1 (HIV-1) activity of a new type of antisense tRNA directed against a nucleotide region in the first coding exon of HIV-1 tat (nucleotides 5924 to 5943; Los Alamos data bank) which is conserved among many HIV-1 clones [4].
  • The role of native contact topology in the folding of a TIM barrel model based on the alpha-subunit of tryptophan synthase (alphaTS) from Salmonella typhimurium (Protein Data Bank structure 1BKS) was studied using both equilibrium and kinetic simulations [5].

Psychiatry related information on Databases

  • The strengths and weaknesses of several of the currently available drug abuse information data bases are reviewed, and qualitative information concerning the scope of contaminants that have been reported in preparations of cocaine, heroin, and phencyclidine is presented [6].

High impact information on Databases

  • Comparison of trigger factor's amino-terminal sequence with those in a computer data bank and with those encoded by sec genes, as well as groEL and heat shock gene dnaK, suggests that trigger factor is encoded by a previously undescribed gene [7].
  • Letter: Data banks for standardized assessments of coma [8].
  • MRC agrees terms of access to gene sequence databank [9].
  • Both proteins have in common their first 196 NH2-terminal amino acids but share little similarity with other sequences in a data bank [10].
  • The recently reported amino acid sequence of rat angiotensinogen was subjected to a computer-assisted search for homology with known sequences stored in a data bank and found to be significantly related to that of plasma alpha 1-antitrypsin, itself a member of a family that includes antithrombin III and ovalbumin [11].

Chemical compound and disease context of Databases

  • This analysis indicates that ranitidine is unlikely to be a common cause of clinically recognized autoimmune hemolytic anemia and demonstrates the utility of large automated medical and pharmacy data bases to conduct post-marketing studies of spontaneously reported drug effects [12].
  • We compared the effectiveness of selectively screening pharmacy data bases to identify patients with hypercholesterolemia with that of mass cholesterol screening [13].
  • PROCEDURE: Meta-analysis of the Food Animal Residue Avoidance Databank was used to generate PPG disappearance curves for cows given single PPG treatments, IM, of 6,600 U/kg (3,000 U/lb) of body weight or 26,400 U/kg (12,000 U/lb), and multiple treatments at 26,400 U/kg (12,000 U/lb), IM [14].
  • METHODS AND RESULTS: We performed a databank analysis of the Total Occlusion Study of Canada (TOSCA), a randomized trial with angiographic follow-up comparing the frequency of reocclusion after angioplasty of a subtotal or total coronary occlusion in patients receiving >/=1 heparin-coated Palmaz-Schatz stent versus balloon angioplasty alone [15].
  • PCR products were displayed on a polyacrylamide gel and fragments showing characteristic alterations in intensity between sarcoidosis and other patients were extracted, sequenced, and compared against Genbank and EMBL DNA data bases [16].

Biological context of Databases


Anatomical context of Databases


Associations of Databases with chemical compounds

  • The coordinates can be derived from experiment (e.g., Cambridge Crystal Database) or be generated from data bases of connection tables (e.g., Cyanamid Laboratories proprietary compounds) via the program CONCORD [27].
  • Coomassie blue-stained, heat-dried, and computer-imaged two-dimensional gels used to develop comprehensive human protein data bases served as the protein source to generate partial amino acid sequences [28].
  • Searches of protein data banks using sequence and structure-based profiles reveal other enzymes, including aminopeptidase P (EC, prolidase (EC, and agropine synthase, that likely share the same "pita-bread" fold common to creatinase and methionine aminopeptidase [29].
  • Data bank searches revealed different groups of proteins sharing the recently identified DXD motif (Busch, C., Hofmann, F., Selzer, J., Munro, J., Jeckel, D., and Aktories, K. (1998) J. Biol. Chem. 273, 19566-19572) and a conserved region defined by a tryptophan residue equivalent to Trp-102 of C. sordellii lethal toxin [30].
  • No significant sequence similarity was found between hexose oxidase and other protein sequences available in data bases [31].

Gene context of Databases

  • The predicted lin-10 protein sequence is not similar to sequences in current data bases, suggesting that lin-10 defines a novel class of gene involved in the specification of cell fates [32].
  • The unc-93 protein has no sequence similarity to proteins listed in current data-bases [33].
  • Metaxin protein is expressed ubiquitously in tissues of the young adult mouse, but no close homologues have been found in the DNA or protein data bases [34].
  • No homology was found between RNA14 and RNA15 or between RNA14 and other proteins contained in data banks [35].
  • SHR5 was cloned, sequenced, and found to encode a 23-kDa protein not significantly homologous to other proteins in the current data bases [36].

Analytical, diagnostic and therapeutic context of Databases

  • Sequence analysis of this cDNA indicates that it encodes a protein of the 425 amino acids [tentatively named adipose differentiation-related protein (ADRP)] that does not have any similarity with sequences contained in the GenBank DNA and Protein Identification Resource protein data bases [37].
  • The cDNA was cloned from a mouse T-cell cDNA library with a probe prepared by PCR using the library and specific PCR primers synthesized based on the reported information of partial amino acid sequences of bovine NTHL1/NTH1 and of EST Data Bases [38].
  • DESIGN AND PARTICIPANTS: From a databank of 299 patients with traumatic brain injury, 18 patients (age range, 17-50 years; median initial Glasgow Coma Scale score, 5) who showed an MRI lesion pattern compatible with pure DAI were identified [39].
  • Data on 584 severely head injured patients with ventriculostomies were prospectively collected in two data banks, The Traumatic Coma Data Bank and The Medical College of Virginia Neurocore Data Bank. These data were retrospectively analyzed for factors associated with ventriculostomy related infections [40].
  • According to data bank assessment, it is hypothesized that the single antidepressant dose of citalopram is to be more than 25 mg, which should be given t.i.d. in clinical trials [41].


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  2. Crystallographic evidence for substrate-assisted catalysis in a bacterial beta-hexosaminidase. Mark, B.L., Vocadlo, D.J., Knapp, S., Triggs-Raine, B.L., Withers, S.G., James, M.N. J. Biol. Chem. (2001) [Pubmed]
  3. A detailed angiographic analysis of patients with ambulatory electrocardiographic ischemia: results from the Asymptomatic Cardiac Ischemia Pilot (ACIP) study angiographic core laboratory. Sharaf, B.L., Williams, D.O., Miele, N.J., McMahon, R.P., Stone, P.H., Bjerregaard, P., Davies, R., Goldberg, A.D., Parks, M., Pepine, C.J., Sopko, G., Conti, C.R. J. Am. Coll. Cardiol. (1997) [Pubmed]
  4. A new antisense tRNA construct for the genetic treatment of human immunodeficiency virus type 1 infection. Biasolo, M.A., Radaelli, A., Del Pup, L., Franchin, E., De Giuli-Morghen, C., Palu, G. J. Virol. (1996) [Pubmed]
  5. Equilibrium and kinetic folding pathways of a TIM barrel with a funneled energy landscape. Finke, J.M., Onuchic, J.N. Biophys. J. (2005) [Pubmed]
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  8. Letter: Data banks for standardized assessments of coma. Jennett, B., Plum, F. N. Engl. J. Med. (1976) [Pubmed]
  9. MRC agrees terms of access to gene sequence databank. Dickson, D. Nature (1995) [Pubmed]
  10. Oncogenic potential of bcl-2 demonstrated by gene transfer. Reed, J.C., Cuddy, M., Slabiak, T., Croce, C.M., Nowell, P.C. Nature (1988) [Pubmed]
  11. Angiotensinogen is related to the antitrypsin-antithrombin-ovalbumin family. Doolittle, R.F. Science (1983) [Pubmed]
  12. Ranitidine-associated autoimmune hemolytic anemia in a health maintenance organization population. Choo, P.W., Goldberg, J.H., Platt, R. Journal of clinical epidemiology. (1994) [Pubmed]
  13. Community pharmacy data bases to identify patients at high risk for hypercholesterolemia. Gardner, S.F., Skelton, D.R., Rollins, S.D., Hastings, J.K. Pharmacotherapy (1995) [Pubmed]
  14. Economic evaluation of risks to producers who use milk residue testing programs. Slenning, B.D., Gardner, I.A. J. Am. Vet. Med. Assoc. (1997) [Pubmed]
  15. Does ticlopidine reduce reocclusion and other adverse events after successful balloon angioplasty of occluded coronary arteries? Results from the Total Occlusion Study of Canada (TOSCA). Berger, P.B., Dzavik, V., Penn, I.M., Catellier, D., Buller, C.E. Am. Heart J. (2001) [Pubmed]
  16. Differential display of messenger RNA expressed in bronchoalveolar lavage cells in pulmonary sarcoidosis patients. Wiwien, H.W., Hiyama, K., Maeda, H., Ishioka, S., Yamakido, M. Hiroshima J. Med. Sci. (1996) [Pubmed]
  17. Interleukin-32: a cytokine and inducer of TNFalpha. Kim, S.H., Han, S.Y., Azam, T., Yoon, D.Y., Dinarello, C.A. Immunity (2005) [Pubmed]
  18. Identification of an autoimmune enteropathy-related 75-kilodalton antigen. Kobayashi, I., Imamura, K., Kubota, M., Ishikawa, S., Yamada, M., Tonoki, H., Okano, M., Storch, W.B., Moriuchi, T., Sakiyama, Y., Kobayashi, K. Gastroenterology (1999) [Pubmed]
  19. Significance of similarities in patterns: an application to beta interferon-related DNA on human chromosome 2. May, L.T., Landsberger, F.R., Inouye, M., Sehgal, P.B. Proc. Natl. Acad. Sci. U.S.A. (1985) [Pubmed]
  20. Cloning and sequencing of a trophoblast-endothelial-activated lymphocyte surface protein: cDNA sequence and genomic structure. Voland, J.R., Wyzykowski, R.J., Huang, M., Dutton, R.W. Proc. Natl. Acad. Sci. U.S.A. (1992) [Pubmed]
  21. Identification and characterization of a RING zinc finger gene (C-RZF) expressed in chicken embryo cells. Tranque, P., Crossin, K.L., Cirelli, C., Edelman, G.M., Mauro, V.P. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  22. Molecular characterization of the murine cytotoxic T-cell membrane glycoprotein Ly-3 (CD8). Panaccio, M., Gillespie, M.T., Walker, I.D., Kirszbaum, L., Sharpe, J.A., Tobias, G.H., McKenzie, I.F., Deacon, N.J. Proc. Natl. Acad. Sci. U.S.A. (1987) [Pubmed]
  23. A new human selenium-containing protein. Purification, characterization, and cDNA sequence. Gladyshev, V.N., Jeang, K.T., Wootton, J.C., Hatfield, D.L. J. Biol. Chem. (1998) [Pubmed]
  24. Protein studies of human non-Hodgkin's B-lymphoma: appraisal by two-dimensional gel electrophoresis. Mohammad, R.M., Maki, A., Vistisen, K., al-Katib, A. Electrophoresis (1994) [Pubmed]
  25. Comparison of coronary artery bypass grafting versus medical therapy on long-term outcome in patients with ischemic cardiomyopathy (a 25-year experience from the Duke Cardiovascular Disease Databank). O'Connor, C.M., Velazquez, E.J., Gardner, L.H., Smith, P.K., Newman, M.F., Landolfo, K.P., Lee, K.L., Califf, R.M., Jones, R.H. Am. J. Cardiol. (2002) [Pubmed]
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  27. Searching for pharmacophores in large coordinate data bases and its use in drug design. Sheridan, R.P., Rusinko, A., Nilakantan, R., Venkataraghavan, R. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  28. Protein-electroblotting and -microsequencing strategies in generating protein data bases from two-dimensional gels. Bauw, G., Van Damme, J., Puype, M., Vandekerckhove, J., Gesser, B., Ratz, G.P., Lauridsen, J.B., Celis, J.E. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  29. Sequence and structure comparison suggest that methionine aminopeptidase, prolidase, aminopeptidase P, and creatinase share a common fold. Bazan, J.F., Weaver, L.H., Roderick, S.L., Huber, R., Matthews, B.W. Proc. Natl. Acad. Sci. U.S.A. (1994) [Pubmed]
  30. Involvement of a conserved tryptophan residue in the UDP-glucose binding of large clostridial cytotoxin glycosyltransferases. Busch, C., Hofmann, F., Gerhard, R., Aktories, K. J. Biol. Chem. (2000) [Pubmed]
  31. Hexose oxidase from the red alga Chondrus crispus. Purification, molecular cloning, and expression in Pichia pastoris. Hansen, O.C., Stougaard, P. J. Biol. Chem. (1997) [Pubmed]
  32. The Caenorhabditis elegans gene lin-10 is broadly expressed while required specifically for the determination of vulval cell fates. Kim, S.K., Horvitz, H.R. Genes Dev. (1990) [Pubmed]
  33. The Caenorhabditis elegans unc-93 gene encodes a putative transmembrane protein that regulates muscle contraction. Levin, J.Z., Horvitz, H.R. J. Cell Biol. (1992) [Pubmed]
  34. Metaxin, a gene contiguous to both thrombospondin 3 and glucocerebrosidase, is required for embryonic development in the mouse: implications for Gaucher disease. Bornstein, P., McKinney, C.E., LaMarca, M.E., Winfield, S., Shingu, T., Devarayalu, S., Vos, H.L., Ginns, E.I. Proc. Natl. Acad. Sci. U.S.A. (1995) [Pubmed]
  35. Mutations in the yeast RNA14 and RNA15 genes result in an abnormal mRNA decay rate; sequence analysis reveals an RNA-binding domain in the RNA15 protein. Minvielle-Sebastia, L., Winsor, B., Bonneaud, N., Lacroute, F. Mol. Cell. Biol. (1991) [Pubmed]
  36. Mutations in the SHR5 gene of Saccharomyces cerevisiae suppress Ras function and block membrane attachment and palmitoylation of Ras proteins. Jung, V., Chen, L., Hofmann, S.L., Wigler, M., Powers, S. Mol. Cell. Biol. (1995) [Pubmed]
  37. Isolation and characterization of a full-length cDNA coding for an adipose differentiation-related protein. Jiang, H.P., Serrero, G. Proc. Natl. Acad. Sci. U.S.A. (1992) [Pubmed]
  38. Cloning and characterization of a mouse homologue (mNthl1) of Escherichia coli endonuclease III. Sarker, A.H., Ikeda, S., Nakano, H., Terato, H., Ide, H., Imai, K., Akiyama, K., Tsutsui, K., Bo, Z., Kubo, K., Yamamoto, K., Yasui, A., Yoshida, M.C., Seki, S. J. Mol. Biol. (1998) [Pubmed]
  39. Cognitive sequelae of diffuse axonal injury. Scheid, R., Walther, K., Guthke, T., Preul, C., von Cramon, D.Y. Arch. Neurol. (2006) [Pubmed]
  40. Ventriculostomy infections: the effect of monitoring duration and catheter exchange in 584 patients. Holloway, K.L., Barnes, T., Choi, S., Bullock, R., Marshall, L.F., Eisenberg, H.M., Jane, J.A., Ward, J.D., Young, H.F., Marmarou, A. J. Neurosurg. (1996) [Pubmed]
  41. CNS effects of citalopram, a new serotonin inhibitor antidepressant (a quantitative pharmaco-electroencephalography study). Itil, T.M., Menon, G.N., Bozak, M.M., Itil, K.Z. Prog. Neuropsychopharmacol. Biol. Psychiatry (1984) [Pubmed]
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