Databases results display

Y. Ralchenko and D. Humbert have developed prototype search engine to carry out the search of a number of remote databases. With this search engine, a user enters a request once only. The request is reformulated by the search engine for each of a number of different database interfaces at different institutions. The requests are sent to databases selected by the user. The search engine gathers the responses from each database and displays the results to the user. Information on each database is available as are links to the databases. 

Since the first annual comparative database report, published in 2007, which included data voluntarily submitted from 382 US hospitals, the number of hospitals and staff respondents included in the database report has grown each year. The Hospital SOPS 2012 Comparative Database Report displays results from 1,128 hospitals and 567,703 hospital staff respondents (Sorra et al. 2012). This large number of hospitals provides for a much more reliable and comprehensive set of benchmarks. 

As already mentioned (Section 5.3), the stored structure information in this type of database makes it possible to search for chemical structures in several ways. One method is to draw a structure (via a molecule editor) and to perform either a precise structure search (full structure search) or a search containing part of the input structure (substructure search) (see Sections 6.2-6.4). The databases also allow the searching of chemical names and molecular formulas (see Section 6.1). The search results are in most cases displayed in a graphical manner. 

Personal computers have introduced new ways to handle pdvate biblographic and text files. The most important factors to consider to achieve satisfactory results in building a bibhographic or text database are the type of information to be stored and the needs of the user. Types of information include correspondence, research results and documentation, meeting notes, and bibliographic references. Needs of the user to be considered should include the potential number of users of the database, restrictions for the access and display of the information because of privacy or proprietary reasons, and the retrieval mechanisms (eg, by keyword, authority list, controUed vocabulary, author, tide, date, or other document or information attributes). In addition, criteria for selecting and encoding information for the database need to be established. 

Another important feature of a LIMS DBMS is the abiUty to perform ad hoc database queries. It is impossible to predict all the forms in which LIMS users will want to display their data while the LIMS is being designed. As a result, it is desirable to select a LIMS which allows users to define their own reports. Most commercial DBMS have a standard query language (SQL) interface. SQL is a simple database query tool which is based on... 

Figure 12 ModBase, a database of comparative protein stracture models. Screenshots of the following ModBase panels are shown A form for searching for the models of a given protein, summary of the search results, summary of the models of a given protein, details about a single model, alignment on which a given model was based, 3D model displayed by RASMOL [237], and a model evaluation by the Prosall profile [217],...

In the case of being successful in calculating multiple conformations by using time- or ensemble-averaged MD restraints the solved molecular structures are presented as 3D models and can be deposited in an electronic structure database (17). Finally, it is recommended to provide an accurate explanation of the procedures used for the structure elucidation because the application of different methods (NMR, DG, MD, SA, Monte-Carlo calculations. X-ray crystallography) may result in varying conformational models which do not implicitly display the real state of a molecule. This aspect should be always kept in mind when dealing with structure determination methods. 

The results of the various semi-empirical calculations on the reference structures contained within the JSCH-2005 database (134 complexes 31 hydrogen-bonded base-pairs, 32 interstrand base pairs, 54 stacked base pairs and 17 amino acid base pairs) are summarised in Table 5-10. The deviations of the various interaction energies from the reference values are displayed in Figure 5-5. As with the S22 training set, the AMI and PM3 methods generally underestimate the interactions whereas the dispersion corrected method (PM3-D) mostly over-estimates the interactions a little. Overall the PM3-D results are particularly impressive given that the method has only... 

Figure 5.5. Search result of monosaccharide database. The web site provides 2D and 3D structures of monosaccharides. The chair conformer of methyl 2-amino-2-deoxy-/ -D-glucopyranoside in which all hydroxy (1-methoxy and 2-amino) groups are equatorial is displayed.

The ProtSite search can be conducted at ScanProsite tool (selecting Scan a sequence for the occurrence of PROSITE patterns) of ExPASy Proteomic tools (http //www.expasy.ch/tools/scnpsite.html), or PPSearch of EBI (http //www2.ebi.ac. uk/ppsearch/) or ProfileScan server (http //www.isrec.isb-sib.ch/software/PFSCAN form.html). On the search form, paste the query sequence, select options (e.g., display in PPSearch and databases in ProfileScan) and click the Run/Start the Scan button. The search results are returned (after clicking SEView applet button in ProfileScan) with different outputs as shown in Figure 12.16. 

Computational results were obtained using Spartan 08 (Wavefunction Inc., Irvine, CA) and software programs from Accelrys Software Inc. with graphical displays generated by the Discovery Studio Visualizer. Where protein structures have been downloaded from the RCSB Protein Data Bank the full references and PDB IDs have been given. I wish to acknowledge the use of the Chemical Database Service at Daresbury for access to other crystal structures. Again, full primary sources can be found in the references. 

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