Editing ValidatorDB:Database organization (section)

=Synopsis page=

The '''ValidatorDB''' synopsis page contains a brief description of '''ValidatorDB''', along with information about the last database update (date and number of structures that have been processed during the validation). Specifically, in May 2014, over 100,000 PDB entries had been processed, containing over 230,000 molecules relevant for validation, and approximately 17,000 different models were used as reference during validation.

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--><center>[[File:VDB_intro.png| 650px]]
 |<!--Col2-->[[File:VDB_samples.png| 650px]]
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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]]''.
 |}

The '''ValidatorDB''' synopsis page further provides access to various data sets. You may retrieve specific validation reports using the '''[[ValidatorDB:Database_organization#Search | Search]]''' tab. Further, the results from PDB-wide validations are available via 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]]'''. A full description of each of these tab is given in their respective sections.


==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 specific validation reports via the '''Search tab'''. 

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 PDB entry and molecule annotation. The syntax of the search 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. In each case, there will be an input field where you can enter a comma or new line separated list of 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 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 '''ValidatorDB''', organized and made accessible via a unique ''[[ValidatorDB:Database_organization#Specifics_page | specifics page]]'', which you can access at a later time via its unique URL. The ''[[ValidatorDB:Database_organization#Specifics_page | specifics page]]'' is described in detail in the second part of the ''Data organization'' section of this manual.

The last 10 searches you performed are listed for your convenience.


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==Overview==
[[File:VDB_overview.png|thumb|right|650px|The '''Overview tab''' contains an overall validation report for all the ligands and non-standard residues in the Protein Data Bank. Each bar represents overall statistics for the [[ValidatorDB:Database_contents | results ]] of a certain type of [[ValidatorDB:Principles#Validation_analyses | validation analysis ]]. ]]

The '''Overview''' tab of the ''synopsis page'' provides a very general statistical evaluation of results across the entire PDB in graphical form. The graph summarizes the results for each type of [[ValidatorDB:Principles#Validation_analyses | validation analysis ]], for all validated molecules, irrespective of annotation or PDB entry. 

Each colorful bar refers to the number of molecules which exhibited issues (missing atoms, wrong chirality, etc.), or fared well (complete structure, correct chirality, etc.) during a given analysis. The length of the bar correlates with the percentage calculated from the total number of molecules analyzed. A bar appears in the '''Overview''' graph only if it represents at least 0.5%. 

Results can be interpreted using the information in the [[ValidatorDB:Database_contents | Database contents]]. Tool tips are available for each element of the graph. 

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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==Details by molecule==

[[File:VDB_Residues.PNG|thumb|right|650px|The '''Details by molecule''' tab contains an interactive table summarizing the results for sets of molecules sharing the same annotation (3-letter code). Each row recapitulates PDB-wide validation results for each such set of molecules. For a given annotation, each column gives the number or percentage of validated molecules which exhibited issues or fared well during a certain [[ValidatorDB:Principles#Validation_analyses | validation analysis ]].]]

The '''Details by Residue''' tab contains an interactive table summarizing the results for sets of molecules sharing the same annotation (3-letter code). Each row recapitulates PDB-wide validation results for all molecules sharing a particular annotation (3-letter code). For a given annotation, each column refers to the results from a specific validation analysis. Each cell gives the number (or percentage) of molecules which exhibited issues (missing atoms, wrong chirality, etc.), or fared well (complete structure, correct chirality, etc.) during a given analysis. 

The table is interactive, allowing efficient sorting and filtering of the results, and direct access to more detailed validation reports for the entries of interest. By default, only the results of some analyses are included in the table. The complete list of analyses available in '''ValidatorDB''' is given below the table. You may customize the table by adding or removing columns which refer to a certain validation analysis. Clicking on any element in the table header allows to sort the table entries according to that element. The filter at the top right corner allows to retrieve only the results for molecules with certain annotations. Regular expressions may be used.

Click on any molecule annotation (3-letter code) in order to access the '''ValidatorDB''' ''specifics page'' with detailed validation results for all molecules in the PDB which share that particular annotation.

Results can be interpreted using the information in the [[ValidatorDB:Database_contents | Database contents]]. Tool tips are available for each element of the table header. 

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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==Details by PDB entry==

[[File:VDB_PDBEntries.PNG|thumb|right|650px|The '''Details by PDB entry''' tab contains an interactive table summarizing the results for sets of molecules originating from the same PDB entry. Each row recapitulates the validation results for all relevant molecules in a single PDB entry. For a given PDB entry, each column gives the number or percentage of validated molecules which exhibited issues or fared well during a certain [[ValidatorDB:Principles#Validation_analyses | validation analysis ]].]]

The '''Details by PDB Entry''' tab contains an interactive table summarizing the results for sets of molecules sharing the same PDB entry. Each row corresponds to one PDB entry, identified by its PDB ID (4-letter code). For a given PDB entry, each column refers to the results from a specific validation analysis. Each cell gives the number (or percentage) of molecules which exhibited issues (missing atoms, wrong chirality, etc.), or fared well (complete structure, correct chirality, etc.) during a given analysis. 

The table is interactive, allowing efficient sorting and filtering of the results, and direct access to more detailed validation reports for the entries of interest. By default, only the results of some analyses are included in the table. The complete list of analyses available in '''ValidatorDB''' is given below the table. You may customize the table by adding or removing columns which refer to a certain validation analysis. Clicking on any element in the table header allows to sort the table entries according to that element. The filter at the top right corner allows to retrieve only the results for molecules with certain annotations (3-letter codes), or originating from PDB entries with certain PDB IDs (4-letter codes). Regular expressions may be used.

Click on any PDB entry in order to access the '''ValidatorDB''' ''specifics page'' with detailed validation results for all molecules in that specific PDB entry.

Results can be interpreted using the information in the [[ValidatorDB:Database_contents | Database contents]]. Tool tips are available for each element of the table header. 

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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