Database analysis

Time Systems, McGraw-HiU, New York, 1985 Hawryszldewycs, Database Analysis and Design, Science Research Associates Inc., Chicago, 1984 Kham-hata, Microprocessois/Microcomputers Architecture, Software, and Systems, 2d ed.. Whey, New York, 1987 Liptak, Instrument Engineers Handbook, Chilton Book Company, Philadelphia, 1995 Melhchamp (ed.), Real-Time Computing with Applications to Data Acquisition and Control, Van Nostrand Reinhold, New York, 1983. 

Branchini, B. R., Lusins, J. O., and Zimmer, M. (1997). A molecular mechanics and database analysis of the structural preorganization and activation of the chromophore-containing hexapeptide fragment in green fluorescent protein. /. Biomol. Struct. Dyn. 14 441-448. 

Edgell ET, Hylan TR (1997). Economic outcomes associated with initial treatment choice in depression a retrospective database analysis. Am J Managed Care 5, S51. 

Hall, L. H., Kier, L. B. Molecular connectivity chi indices for database analysis and structure-property modeling. In Topological Indices and Related Descriptors in QSAR and QSPR, Devillers,... 

Piecoro LT, Browning SR, Prince TS et al. (2000) A database analysis of potentially inappropriate drug use in an elderly medicaid population. Pharmacotherapy 20(2) 221-228 Ray WA, Thapa PB, Gideon P (2000) Benzodiazepines and the risk of falls in nursing home residents. J Am Geriatr Soc 48(6) 682-685... 

Caro JJ, Ward A, Levinton C, Robinson K. The risk of diabetes during olanzapine use compared with risperidone use a retrospective database analysis. J Clin Psychiatry 2002 63(12) 1135-9. 

Based on the integrated PK database analysis, CL values were estimated and are displayed in Fig. 14.6 as a function of the cetuximab serum concentrations. A concentration-dependent decrease in CL was observed in the integrated PK database analysis, similar to that observed in the non-compartmental analysis. 

The Protein Data Bank (PDB) is the primary structure database serving as the international repository for the processing and distribution of 3D structures of biomacromolecules (Bernstein et al, 1977). The database is operated by the Research Collaboratory for Structural Bioinformatics (RCSB) and is accessible from the primary RCSB site at http //www.rcsb.org/pdb/ (Berman et al., 2000). Most of the structure fold/motif/domain databases (Conte et al., 2000) and analysis servers (Brenner et al, 2000 Hofmann et al, 2000 Kelley et al., 2000 Shi et al., 2001) utilize 3D-structure information from PDB and sequence information from primary sequence databases. Some of these databases/analysis servers and their URL are listed in Table 12.3. 

Zhang Q, Wang P, Kim Y et al (2008) Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res 36 W513-W518... 

Sanz EJ, De Las-Cuevas C, Bate A, Edwards R. Selective serotonin reuptake inhibitors in pregnant women and neonatal withdrawal syndrome a database analysis. Lancet 2005 365 482-87. 

More recently, Mota-Sanchez et al. (2002) found a similar trend using database analysis. Table 10.3 shows that the majority of reported cases of resistance are arthropod resistance to organophosphate (44%) and organochlorine (32%) insecticides. It is understandable, because these two classes of insecticides have been used in pest control for over half a century. As shown in Table 10.4, twelve species of insects have developed resistance to various strains of Bt and Bt toxins in the laboratory and/or the field. 

L. Fabian, Cambridge structural database analysis of molecular complementarity in cocrystals, Cryst. Growth Des. 9 (2009) 1436-1443. 

Different methods exist that predict protein secondary stmcture elements from chemical shift values [e.g.. Chemical Shift Index (CSI) (3) and Probability-based protein Secondary Stmcture Identification using combined NMR chemical-shift data (PSSI)] (4). These methods are based on the statistics of database analysis of chemical shift values from a range of peptides and proteins of known secondary stmcture. Chemical shifts have also been used to predict backbone torsion angles by software such as Torsion Angle Likelihood Obtained from Shifts and Sequence similarity (TALOS) (5). 

Low energy conformations of the Ala-cisPro-Tyr peptide that display a c/sproline-aromatic interaction were found by structural database analysis and systematic search (see section 3 and Figure 3). In order to know whether these conformations are stable in water on a 100 ps time scale, five MD simulations started from the conformations al-3 and bl-2 were performed. The same MD protocol as for the long MD simulations was used, with 100 ps equilibration time and 100 ps data acquisition time. 

Gillon, A.L. Feeder, N. Davey, R.J. Storey, R. Hydration in molecular crystals—a Cambridge structural database analysis. Cryst. Growth Des. 2003, 3, 663-673. 

In an FDA database analysis, 346 cases of cardiac dysrhythmias associated with erythromycin were identified. There was a preponderance of women, as there was among those with life-threatening ventricular dysrhythmias and deaths after intravenous erythromycin lactobionate. A sex difference in cardiac repolarization response to erythromycin is a potential contributing factor, since in an in vitro experiment on rabbit hearts, erythromycin caused significantly greater QT prolongation in female than in male hearts (7). 

In a retrospective database analysis 25 cases of torsade de pointes associated with ciprofloxacin (n = 2), ofloxacin (n = 2), levofloxacin (n = 13), and gatifloxacin (n = 8) were identified in the USA (28). Ciprofloxacin was associated with a significantly lower rate of torsade de pointes (0.3 cases/10 million prescriptions) than levofloxacin (5.4/10 million) or gatifloxacin (27/10 million). When the analysis was limited to the first 16 months after initial approval of the drug, the rates for levofloxacin (16/10 million) and gatifloxacin (27/10 million) were similar. 

Bawden, D. (1990). Applications of Two-Dimensional Chemical Similarity Measures to Database Analysis and Querying. In Concepts and Applications of Molecular Similarity (Johnson, M.A. and Maggiora, G.M., eds.), Wiley, New York (NY), pp. 65-76. 

Bernard, P, Golbraikh, A., Kireev, D.B., Chretien, J.R. and Rozhkova, N. (1998). Comparison of Chemical Databases Analysis of Molecular Diversity with Self Qrganizing Maps (SOM). Ana-lusis, 26,333-341. 

Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B. Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res. 2008 36 W513-W518. Epub 2008 May 31. 

Long, N., Mestayer P.G., and Kergomard, C. (2003) Urban database analysis for mapping morphology and aerodynamic parameters the case of St Jerome suburban area, in Marseille during ESCOMPTE, Proceedings of the Fifth International Conference on Urban Climate, September 1-5 2003, Lodz, Poland. 

Gillon AL, Feeder N, Davey ly, and Storey R, Hydration in Molecular Crystals-A Cambridge Structural Database Analysis. Cryst Growth Des 2003 3 663-673. 

Fgenesh+ was used to improve the accuracy of prediction for 49 genes. 37 of them were predicted using D. melanogaster s own proteins, already deposited in protein databases. Analysis of these predictions demonstrates that even for such cases prediction of accurate gene structure may not be trivial, although in most cases Fgenesh+ improved the prediction accuracy relative to ab initio methods. 

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