PMC:540055 / 8317-11630 JSONTXT

{"project":"2_test","denotations":[{"id":"15608266-11337471-76789792","span":{"begin":1796,"end":1798},"obj":"11337471"},{"id":"15608266-10087920-76789793","span":{"begin":1878,"end":1880},"obj":"10087920"},{"id":"15608266-14681353-76789794","span":{"begin":2107,"end":2108},"obj":"14681353"},{"id":"15608266-12520024-76789795","span":{"begin":2126,"end":2128},"obj":"12520024"},{"id":"15608266-3547335-76789796","span":{"begin":2265,"end":2267},"obj":"3547335"},{"id":"15608266-7108955-76789797","span":{"begin":2300,"end":2302},"obj":"7108955"}],"text":"NAVIGATION OF THE DATABASE\nThe interface of DynaProt 2D consists of three parts: the search including the resultset, the interactive reference maps and the summarized protein information table. The search and resultset serve as main interface for navigation and thus, are permanently available on the left side of the screen (Figure 2). The interactive reference maps and the summarized protein information table both comprise manifold information. Therefore, the user can intuitively switch between these two pages, which make up most of the screen on the right-hand side of the Internet browser (Figure 2).\nThe search through the database is dominated either by six different parameters or by interactive exploration of the reference maps. As parameters, full or partial names of genes, proteins or identifiers are supported, as well as ranges of Mr and pI. Furthermore, the search can be limited to a selected 2D reference map too. After submission of the search request, all proteins, which fit the parameters, are indicated in the resultset. In contrast, the interactive reference maps present all identified proteins on a 2D gel at one sight. By positioning the mouse over the red encircled spots, information about the spots, namely protein name, identifier and spot ID, are displayed. On clicking, the summarized protein information of the selected spot is presented in the Internet browser. Below the reference gel, detailed information about growth conditions, protein extraction, IPG-DALT conditions and references are provided (Figure 2).\nThe summarized protein information provides the full-length protein name, gene identifier, predicted pI and Mr as well as the functional classification according to the annotation on the MOLOKO website (http://spock.jouy.inra.fr/RL000801.html) (12), and the predicted cellular localization calculated with the PSORT algorithm (13). Links to individual or all spots of the selected protein are implemented to switch from protein information to highlighted spots on reference gels. Furthermore, two widely used identifiers link to the corresponding GenBank (9) and Swiss-Prot (15) database entries. The codon adaptation index and the grand average of hydropathicity value give information about expected expression (16) and solubility of the protein (17). Finally, the complete protein sequence can be retrieved for further analyses and calculations.\nThe sophisticated navigation and management by the embedded PHP scripts (Figure 1) makes the database on the web server independent of any decentralized software. Thus, the database can be accessed and maintained from every computer connected to the Internet, simply by using a web browser. Protein information is administered online by PHPMyAdmin. Gel images are uploaded in the PNG file format. The addition of gels, experimental data and spot coordinates to the database is supported by an administrative PHP script, which can be accessed only by collaborating laboratories, e.g. mass spectrometry service stations or other registered users. This solution was chosen, because the latter data are more frequently added or changed. The administrative PHP script resembles a form in which the data and spot coordinates are copied. By submission of the form, the newly added data are immediately accessible online."}