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ValidatorDB:Database organization

89 bytes removed, 21:57, 20 October 2014
Custom search
==Custom searchSearch==
[[File:VDB_CustomValidatorDB-Search By Entry and Annotation.PNGpng|thumb|right|650px|The '''Custom search Search tab''' allows to retrieve validation reports for specific molecules. You may use several search criteria, namely by PDB entry (4-letter code), according to by molecule identifier (PDB ID: residue ID chain), molecule annotation (3-letter code) and , or a combination of the PDB entryand molecule annotation (shown here). In each case you will be provided with an input field, where you can enter a list of values for the relevant criterion. Examples and tool tips are provided for easy reference with respect to the expected syntax.]]
Additionally, the ''synopsis page'ValidatorDB''' allows to access the contains validation results for specific residues of interest via the '''Quick Lookup bar''' at the bottom of the pageentire Protein Data Bank. Simply type You are probably interested only in a comma separated list subset of residue annotations these (3-letter codes) into the '''Quick Lookup bar'''e.g., and you will be redirected to the [[ValidatorDB:Database_organization#Specifics_page | specifics page]] containing validation results for a specific inhibitor which appears in the molecules PDB entry you requestedplan to use further in your simulations). If you specify a list of PDB IDs (4-letter codes) instead, then the corresponding [[ValidatorDB:Database_organization#Specifics_page | specifics The ''synopsis page]] will contain '' allows to access specific validation results for all relevant molecules in reports via the PDB entries you specified'''Search tab'''.
In addition to You may define the predefined summaries and reports already describedsearch using several criteria, '''ValidatorDB''' can generate custom validation reports using the '''Custom Search''' functionality. Such custom validator reports allow you better focus on molecules of interest namely PDB entry (drug molecules4-letter code), polycyclic moleculesmolecule identifier (PDB ID: residue ID chain), etc.molecule annotation (3-letter code), from relevant or a combination of the PDB entries (entries with a resolution higher than 2 Åentry and molecule annotation. The syntax of the search is quite simple, published after 2010, etc.)but you can always check out the examples and tool tips if you want to make sure.
You may specify Click on criterion you plan to use. In each case, there will be an input field where you can enter a set comma or new line separated list of molecules using PDB IDs (4-letter codes) and annotations (3-letter codes)values for the relevant criterion. Alternatively, you You may prefer to use the advanced search functions available on the Protein Data Bank web page, in order to generate a list of relevant annotations and PDB IDs. Instructions on how to achieve this are included in the web page as a tool tip.
The validation results for the molecules you specified according to the chosen criteria are then retrieved from '''ValidatorDB''', organized and made accessible in the same manner as the above described tabs, namely 'via a unique ''[[ValidatorDB:Database_organization#Overview Specifics_page | Overviewspecifics page]]''', 'which you can access at a later time via its unique URL. The ''[[ValidatorDB:Database_organization#Details_by_molecule Specifics_page | Details by moleculespecifics page]]''is described in detail in the second part of the ', and 'Data organization''[[ValidatorDB:Database_organization#Details_by_PDB_entry | Details by PDB entry]]'''. The only difference is that the statistics will refer to your selection, and not to the entire PDB. Moreover, section of this custom snippet of the database will be accessible at its own URL for some time, so that you can return to it later onmanual.  The last 10 searches you performed are listed for your convenience.

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