Check-list 6,149 - retrieval

The common atomic coordinate files for 3D structure in biochemistry is PDB format. The pdb files of polysaccharides, proteins, and nucleic acids can be retrieved from the Protein Data Bank at RCSB (http //www.rcsb.org/pdb/). On the home page (Figure 4.15), enter PDB ID (check the box query by PDB id only ) or keywords (check the box match exact word ) and click Find a structure button. Alternatively, initiate search/retrieval by selecting SearchLite. On the query page, enter the keyword (e.g., the name of ligand or biomacromolecule) and click Search button. Select the desired entry from the list of hits to access Summary information of the selected molecule. From the Summary information, select Download/Display file and then PDB Text and PDB noncompression format to retrieve the pdb file. In order to display 3D structure online, choose View structure followed by selecting one of 3D display options. The display can be saved in. jpg or. gif image format. 

An automated retrieval system which benefits from the frame type representation has been developed to easily and rapidly access any data in a transparent way for the user. He only needs to indicate his choice among the propositions suggested by the system. The program has been designed so that constraints can be put on any parameter in order to select distinct experiments. For example, to analyze which zeolite is the most suitable for a given chemical reaction at given reaction conditions, the user will put successive constraints on the kind of reaction, the type of zeolite, the limits of conversion and selectivity, and on the reaction conditions. After each selection, the system displays the number of experiments which satisfy these constraints. Hence, the user can decide to i) list the selected experiments, ii) impose a new selection by entering an additional constraint, iii) plot the retained data, iv) compute correlations, or v) quit the application. One can then easily access the characteristics of the listed experiments so that the user can check and compare all the parameters and verify which one(s) could influence the observed conversion, selectivity, and yield, and maybe have a track for further analyses. 

In batch processes, these search formulations are keypunched on to cards and read into the computer. An editing process checks the validity of the terms against a dictionary the search process then retrieves a list of relevant references from the inverted file and finally a print program retrieves these references and prints them out in intelligible form. 

The CAS number for a chemical is probably listed on the label if you are retrieving a chemical from the bottle or container in which it was received from a chemical supply company. But, to more generally find a CAS number, it is easy to access reliable web sites. Examples of two such web sites are Chemlndustry.com (http //www.chemindustry.com/ apps/chemicals) and the National Institutes of Standards and Technology (http //webbook.nist.gov/chemistry/). At these sites you can search by name or formula to find a CAS number. Safety Data Sheets (Section 3.1.3) will also have the CAS number. See the SDS in Appendix A and look in Section 1 to find the CAS number. And this is one instance where you can probably also trust the Wrkipedia information about a chemical In fact, for Wikipedia entries about chemicals you will notice that in the boxed column of basic information about the chemical, you will find a green check mark (/) to indicate that the entry has been verified. 

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