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In '''ValidatorDB''', the results of the validation analyses are organized systematically, ranging from detailed reports for single molecules, to a PDB-wide general summary, and fully customized reports. To facilitate interpretation, access is provided in graphical and tabular form via different sections of the web interface.
'''ValidatorDB''' is organized on two main levels, namely PDB-wide validation statistics (synopsis page), and detailed validation reports for specific molecules of interest (specifics page). We shall describe each level of the database in detail below. The database or various sections of it can be downloaded in .csv or .JSON format, along with the 3D structure files of all models, input motifs and validated molecules.
=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.
==Overview==
[[File:VDB_overview.png|thumb|right|500px650px|The ''synopsis page'Overview tab''' consists of 6 tabs, two providing support, contains an overall validation report for all the ligands and four enabling access to non-standard residues in the Protein Data Bank. Each bar represents overall statistics for the database itself[[ValidatorDB:Database_contents | results ]] of a certain type of [[ValidatorDB:Principles#Validation_analyses | validation analysis ]]. ]] The support tabs '''Quick HelpOverview''' and tab of the ''synopsis page'Samples''' help you get started, with basic information and examples provides a very general statistical evaluation of database snippetsresults across the entire PDB in graphical form. Various interactive guides are accessible by a green button at The graph summarizes the top right corner results for each type of some tabs.[[ValidatorDB:Principles#Validation_analyses | validation analysis ]], for all validated molecules, irrespective of annotation or PDB entry.
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==Details by molecule==
[[File:VDB_Residues.PNG|thumb|right|500px650px|The ''synopsis page'Details by molecule''' consists tab contains an interactive table summarizing the results for sets of 6 tabs, two providing support, and four enabling access to molecules sharing the database itselfsame annotation (3-letter code). The support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples Each row recapitulates PDB-wide validation results for each such set of database snippetsmolecules. Various interactive guides are accessible by For a green button at given annotation, each column gives the top right corner number or percentage of some tabsvalidated 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 '''Details by Residue''' tab contains an table is interactive table summarizing , allowing efficient sorting and filtering of the results , and direct access to more detailed validation reports for each residue validated across the entire PDBentries of interest. Each row corresponds to one residueBy default, identified by its residue name (3-letter code). The information only the results of some analyses are included in the table is organized according to the [[ValidatorDB:Analysis_of_Results|validation result]]. The color coding for the table header and the font inside the table is the same as in the categories defined complete list of analyses available in the '''OverviewValidatorDB''' tabis given below the table. Each You may customize the table by adding or removing columns which refer to a certain validation analysis. Clicking on any element of in the table header is described in a tool tip, but note allows to sort the table entries according to that here element. The filter at the term residue actually refers top right corner allows to occurrence of residue (motif)retrieve only the results for molecules with certain annotations. Regular expressions may be used.
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==Details by PDB entry==
[[File:VDB_PDBEntries.PNG|thumb|right|500px650px|The ''synopsis page'Details by PDB entry''' consists tab contains an interactive table summarizing the results for sets of 6 tabs, two providing support, and four enabling access to molecules originating from the database itselfsame PDB entry. The support tabs '''Quick Help''' and '''Samples''' help you get started, with basic information and examples of database snippetsEach row recapitulates the validation results for all relevant molecules in a single PDB entry. Various interactive guides are accessible by For a green button at given PDB entry, each column gives the top right corner number or percentage of some tabsvalidated 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 all residues validated in each sets of molecules sharing the same PDB entry. Each row corresponds to one PDB entry, identified by its PDB ID (4-letter code). The information in the table is organized according For a given PDB entry, each column refers to the [[ValidatorDB:Analysis_of_Results|results from a specific validation result]]analysis. The color coding for Each cell gives the table header and the font inside the table is the same as in the categories defined in the '''Overview''' tabnumber (or percentage) of molecules which exhibited issues (missing atoms, wrong chirality, etc. Each element of the table header is described in a tool tip), but note that here the term residue actually refers to occurrence of residue or fared well (motifcomplete 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. Click on any PDB in order The filter at the top right corner allows to access retrieve only the '''[[ValidatorDB:Specifics_page| ValidatorDB specifics page]]''' with detailed validation results for all residues in that molecules with certain annotations (3-letter codes), or originating from PDB entries with certain PDB entryIDs (4-letter codes). Regular expressions may be used.
=Specifics page=
The '''[[ValidatorDB]] ''' ''specifics page'' provides detailed validation reports for various selections of the database. Such reports include a validation summary and detailed information in both tabular and graphical form, along with a 3D structure visualizer for closer inspection of the problematic structures. The ''specifics page'' is accessible from the ''[[ValidatorDB:Database_organization#Synopsis_page | synopsis page]]'', either via the '''LookUp bar''' on the '''OverviewQuick Lookup''' tabbar, or via the residue names and PDB IDs any single entry in the interactive tables on from the tabs '''Details by Residuemolecule''' and '''Details by PDB Entryentry''', respectively. Depending on how it was accessed, the '''specifics page''' might retrieve validation results for one or more residuesmolecules, a fact mentioned at the very top of the page. The validation results are accessible in tabular and graphical form via several tabs on the ''specifics page'', namely '''Overview''', '''Summary''', '''Details''' and '''Processing Warnings'''. These are described in detail in their respective sections below. It is important to note that the ''specifics page'' contains annotation-based validation reports. This means that if the molecules you selected share the same annotation (3-letter code), all results will be included in a single report. However, you may have retrieved validation results for molecules with different annotations, as is the case with PDB entries containing many different ligands for instance. In this case, the validation results will be organized according to annotation. Specifically, there will be as many reports as there are annotations. All tabs on the ''specifics page'' discuss one report at a time, and allow easy navigation between these reports. The only exception is the '''Overview''' tab, which presents the total statistics for all validated molecules, and not per annotation.
==Overview==
[[File:VDB_Model.png|thumb|right|500px650px|The '''Overview''' tabof the ''specifics page'' provides statistics of the validation results for all selected molecules.]]
To keep consistency with the ''synopsis page'', the '''Overview''' tab on the ''specifics page '' also allows visualization of general validation statistics for a the molecules you selected number of residues via the Overview tab. This representation is entirely compatible with that of the '''Overview''' tab on the ''synopsis page'', and in fact makes up a subset of that data set. All color coding conventions are keptThe green box above the graph indicates the number of validated molecules, and tool tips provide descriptions of each graphical elementtogether with their origin.
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==Summary==
The validation reports available in the '''Summary''' tab of the ''specifics page'' are organized by annotation (3-letter code). You can easily navigate between reports by clicking on the annotation of interest in the bar under the tab names. Each report consists of information about the model and validated molecules corresponding to that particular annotation. {| class="wikitable" border="1" style="margin: 1em auto 1em auto;" |- |<!--Col1-->[[File:VDB_Residue_summary.PNG|thumb650px]] |<!--Col2-->[[File:VDB_Entry_summary.PNG|right650px]] |500px- |<!--Col1-->The '''Summary''' tab]]of the ''specifics page'' for all molecules sharing a '''specific annotation (3-letter code)'''. 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 the ''specifics page'' for a '''single PDB entry''' allows easy navigation between annotation-based<br/> validation reports. Each report consists of a description of the model corresponding to that annotation,<br/> a recapitulation of all validated molecules sharing that 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).
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==Details==
[[File:VDB_Residue_details.PNG|thumb|right|650px|The '''Details''' tab of the ''specifics page'' serves as a filter based on specific results of the validation analyses, and further enables access to a highly detailed validation report for each validated molecule.]]
As already mentioned, the content of the table depends on the filter bar above the table. The validation reports available in the '''Details''' tab is organized into a table where each row contains information regarding a single validated motif. The content of the table (i.e., which motifs ''specifics page'' are included, and what information is displayed) is dictated by the values of three selection fields at the top of the table. Click on the first field, and select the validated residue organized by its name annotation (3-letter code) from . You can easily navigate between reports by selecting the annotation of interest in the leftmost drop down menuin the filter bar under the tab names (above the table). Only the motifs table rows with results for the molecules that were matched to that residue name annotation will be displayed in the table. Click on You may further refine the second field and select filter according to the type of validation issue you are interested in (e.g., wrong metal chirality, missing a specific atom, containing substitutions at a certain position, etc.) . Pick the issue of interest from the corresponding drop down menuin the filter bar. Only the motifs table rows with results for the molecules which exhibit exhibited that type of particular issue will be displayed . Whenever you pick something in a drop down menu of the filter bar, the table. The number of motifs molecules that fit each your selection is given in brackets. If you want to make your selection even more specific, use the selection filed ''Id filter'' at the right of the filter bar.
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==3D visualizationSingle molecule report==[[File:VDB_Details_entry.PNG|thumb|right|500px650px|'Detailed validation report for a '''single molecule''', accessible by clicking on the respective molecule Id in the '''Details''3D'table of the ''specifics page'' visualization . Consists of a full description for the molecule and detailed the model, complete with references, all resultsfrom all validation analyses, and 3D visualization of all structures involved in the validation process.]]
The 3D viewer implemented in the [[ValidatorDB]] interface '''single molecule report''' offers one step further in a complete image of the analysis of validation results for each individual validated motif, and particular molecule. It is accessible via the '''Details''' tab on the ''specifics page. In the table'', simply click by clicking on the Id (unique identifier containing the PDB ID and a serial number) of a motif the molecule of interest . As you open this report, the molecule Id will appear in order to open the top left corner of the report. The '''single molecule report''' starts with two 3D viewervisualizers, where you can inspect the structural inaccuracies more closely. Here you will be able to view and manipulate with the 3D representations of the validated molecule, the input motif , the model, and model residuesuperimpositions of these, in order to help you better assess the position and relevance of the structural issues found during validation(see the full list of terms [[ValidatorDB:Terminology | here]]). AdditionallyAt the top of each visualizer there is a drop down menu where you may choose the structure of interest, along with a few visualization options (atom labels, bonds vs sticks, full screen view). The 2D representation of the model is also provided for clarity, which and is especially helpful for larger motifsmolecules. Basic Beneath the visualizers, the '''single molecule report''' is organized into three columns, but you may have to scroll down to see all the information about in each column. The left column contains the validated motif is also givenfull identification of the molecule in its original PDB entry, the description of the model and full identification in the wwPDB CCD, along with and a complete report list of [[ValidatorDB:Database_contents#Processing_warnings | processing warnings]], if any were encountered during validation. The middle column lists the validation resultsof the ''completeness'' and ''chirality'' analyses, where all and the right column those of the ''advanced'' analyses (see the potential issues full list of validation analyses [[ValidatorDB:Principles#Validation_analyses | here]]). Each problematic atom is listed. The results are listedlabeled 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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==Processing Warnings==
[[File:VDB_Warnings.PNG|thumb|right|500px650px|The '''Processing warnings''' tabof the ''specifics page'' lists unusual circumstances encountered during validation.]]
The validation reports in ValidatorDB ''specifics page'' may also mention various contain the separate tab '''Processing warnings''', which lists unusual aspects circumstances encountered during the validationof each molecule. 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 '''Processing Warnings''' 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 Validation, such as bad two residues being too close together (misused concept of alternate conformations) or unusual bond lengths given by the CONECT records. Make sure that negative validation results (e.g., missing atoms) are not in fact caused by ignoring some atoms in an ill-formed structure.
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'''Continue by examining the [[ValidatorDB:CaseStudies | case studies]], or return to the [[ValidatorDB:UserManual | Table of contents]].'''
