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ValidatorDB:Database organization

1,153 bytes added, 10:03, 28 December 2014
Synopsis page
The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. Since this is your first contact with the database, the support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples of database snippets. Various interactive guides are accessible by a green button at the top right corner of some tabs. Examples of more complex analyses are available as ''[[ValidatorDB:CaseStudies | case studies]]''.
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|<!--Col1-->The ''synopsis page'' consists of 6 tabs, two providing support, and four enabling access to the database itself. The support tab '''Quick Help''' helps you get started, with basic information about how to get oriented in the web page. Various interactive guides are accessible by a green button at the top right corner of some tabs. Tool tips are available for most of the graphical elements.
|<!--Col2--> The '''Samples''' tab offers basic examples of database snippets, along with a brief interpretation of results. Two categories of sample validation reports (Molecules, PDB Entry) illustrate interesting cases of molecules with a high or low number of errors. Additionally, the Step-by-Step category contains video tutorials and slides explaining how to obtain such results. Examples of more complex analyses are available as ''[[ValidatorDB:CaseStudies | case studies]]''.
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The '''ValidatorDB''' synopsis page further provides access to various data sets of . You may retrieve specific validation reports using the '''[[ValidatorDB:Database_organization#Search | Search]]''' tab. Further, the results from PDB-wide validations are available via four three different tabs, namely '''[[ValidatorDB:Database_organization#Overview | Overview]]''', '''[[ValidatorDB:Database_organization#Details_by_molecule | Details by molecule]]''', and '''[[ValidatorDB:Database_organization#Details_by_PDB_entry | Details by PDB entry]]''' and '''[[ValidatorDB:Database_organization#Custom_search | Custom search]]'''. A full description of each of these tab is given in their respective sections.
Additionally==Search== [[File:ValidatorDB-Search By Entry and Annotation.png|thumb|right|650px|The '''Search tab''' allows to retrieve validation reports for specific molecules. You may use several search criteria, namely by PDB entry (4-letter code), by molecule identifier (PDB ID: residue ID chain), molecule annotation (3-letter code), or a combination of the PDB entry and 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.]] '''ValidatorDB''' contains validation results for the entire Protein Data Bank. You are probably interested only in a subset of these (e.g., the validation results for a specific inhibitor which appears in the PDB entry you plan to use further in your simulations). The ''synopsis page'' allows to access the specific validation results for specific residues of interest reports via the '''Quick Lookup barSearch tab''' at .  You may define the search using several criteria, namely PDB entry (4-letter code), molecule identifier (PDB ID: residue ID chain), molecule annotation (3-letter code), or a combination of the bottom PDB entry and molecule annotation. The syntax of the pagesearch is quite simple, but you can always check out the examples and tool tips if you want to make sure. Click on criterion you plan to use. Simply type In each case, there will be an input field where you can enter a comma or new line separated list of residue values for the relevant criterion. 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 (3-letter codes) into and PDB IDs. Instructions on how to achieve this are included in the web page as a tool tip.  Once you click the blue search button at the bottom of the page, the validation results for the molecules you specified according to the chosen criteria are then retrieved from '''Quick Lookup barValidatorDB''', organized and you will be redirected to the made accessible via a unique ''[[ValidatorDB:Database_organization#Specifics_page | specifics page]] containing validation results for the molecules '', which you requestedcan access at a later time via its unique URL. If you specify a list of PDB IDs (4-letter codes) instead, then the corresponding The ''[[ValidatorDB:Database_organization#Specifics_page | specifics page]] will contain validation results for all relevant molecules '' is described in detail in the PDB entries second part of the ''Data organization'' section of this manual. The last 10 searches you specifiedperformed are listed for your convenience.   <br style="clear:both" />
==Overview==
The results for different types of validation analyses are labeled using the unified color scheme: <span style="color:#006400">complete structure and correct chirality</span>, <span style="color:#FF0000">incomplete structure</span>, <span style="color:#DAA520">wrong chirality</span>, <span style="color:#607d8b">warning</span>.
 
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==Custom search==
 
[[File:VDB_Custom.PNG|thumb|right|650px|The '''Custom search tab''' allows to retrieve validation reports for specific molecules, according to annotation (3-letter code) and PDB entry.]]
 
In addition to the predefined summaries and reports already described, '''ValidatorDB''' can generate custom validation reports using the '''Custom Search''' functionality. Such custom validator reports allow you better focus on molecules of interest (drug molecules, polycyclic molecules, etc.), from relevant PDB entries (entries with a resolution higher than 2 Å, published after 2010, etc.).
 
You may specify a set of molecules using PDB IDs (4-letter codes) and annotations (3-letter codes). Alternatively, 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 are then retrieved from '''ValidatorDB''', organized and made accessible in the same manner as the above described tabs, namely '''[[ValidatorDB:Database_organization#Overview | Overview]]''', '''[[ValidatorDB:Database_organization#Details_by_molecule | Details by molecule]]''', and '''[[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, this custom snippet of the database will be accessible at its own URL for some time, so that you can return to it later on. The last 10 searches you performed are listed for your convenience.
 
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==Summary==
[[File:VDB_Residue_summary.PNG|thumb|right|650px|The validation reports available in the '''Summary''' tab of the ''specifics page'' allows easy navigation between are organized by annotation(3-based validation letter code). You can easily navigate between reportsby clicking on the annotation of interest in the bar under the tab names. Each report consists of a description of information about the model and validated molecules corresponding to that particular annotation, a recapitulation of all validated molecules sharing that annotation, statistics for each validation analysis (completeness, chirality, advanced), and statistics for each problematic atom.]]
{| class="wikitable" border="1" style="margin: 1em auto 1em auto;" |- |<!--Col1-->[[File:VDB_Residue_summary.PNG| 650px]] |<!--Col2-->[[File:VDB_Entry_summary.PNG| 650px]] |- |<!--Col1-->The validation reports available in the '''Summary''' tab of the ''specifics page'' are organized by for all molecules sharing a '''specific annotation (3-letter code)'''. You can easily navigate between reports by clicking on The<br/> report consists of a description of the model corresponding to that annotation , a recapitulation of all validated<br/> molecules sharing that annotation, statistics for each validation analysis (completeness, chirality, advanced),<br/> and statistics for each problematic atom. |<!--Col2--> The '''Summary''' tab of interest in the bar under the tab names''specifics page'' for a '''single PDB entry''' allows easy navigation between annotation-based<br/> validation reports. Each report consists of information about a description of the model and corresponding to that annotation,<br/> a recapitulation of all validated molecules corresponding to sharing that particular annotation, statistics for each validation analysis<br/> (completeness, chirality, advanced), and statistics for each problematic atom. |}
First, the model from wwPDB CCD is briefly described by name, molecular formula, 2D structure, etc. Next, a recapitulation of all molecules and their respective PDB entries is also included, followed by a table with results of the main validation analyses (completeness, chirality, advanced). For each validation analysis, statistics are provided for all problematic atoms. Note that here the statistics cover only the molecules sharing this annotation (3-letter code).
==Processing Warnings==
[[File:VDB_Warnings.PNG|thumb|right|650px|The '''Processing warnings''' tabof the ''specifics page'' lists unusual circumstances encountered during validation.]] The ''specifics page'' may also contain the separate tab '''Processing warnings''', which lists unusual circumstances encountered during the validation of each molecule. Sometimes the PDB entries contain information that is ambiguous, conflicting or which deviates strongly from the expected reference.
The validation reports in ValidatorDB also mention various unusual aspects encountered during validation. Sometimes the processed PDB entries contain information that is ambiguous, conflicting or which deviates strongly from the expected reference. [[ValidatorDB]] reports such events as processing warnings. Such information can be found in the Some '''Processing Warningswarnings''' tab on the specifics page. The selection field at the top of the page helps filter the warnings for different residues, in case more of them are in validation report. Simply click on the drop down menu and select the category of warnings that you would like to explore. Processing warnings are issues that may cause incorrect Validationvalidation, such as bad two residues molecules being too close together in the 3D space, or some atoms being too far (misused concept disconnected) from the rest of alternate conformations) or unusual bond lengths given by the CONECT recordsmolecule. Such structures are generally marked as ''degenerate'' in the ''completeness'' analyses. Make sure that negative Other '''processing warnings''' are only meant to inform of which course of action was taken during validation results (e.g., missing atomswhich conformer was validated if several conformers of that molecule were present in the original PDB entry) are not in fact caused by ignoring some atoms in an ill. The drop down menu at the top of the page helps filter the warnings for molecules with a specific annotation (3-formed structure....include degenerate..letter code).
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'''Continue by examining the [[ValidatorDB:CaseStudies | case studies]], or return to the [[ValidatorDB:UserManual | Table of contents]].'''

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