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==
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=Specifics page=Custom search== [[File:VDB_Custom.PNG|thumb|right|650px|The '''Custom search tab''' Search the database for validation results corresponding to specific PDB entries and molecules of interest.[[ValidatorDB]] The '''Custom Search''specifics page'' tab allows you to create your own view of the ligands provides detailed validation reports for various selections of the PDB database. Simply paste Such reports include a list of your desired ligands (3-letter code) validation summary and/or PDB entries (4-letter code) detailed information in provided text boxes separated by commas or a newlines. This is particularly convenient in case you need to retrieve both tabular and graphical form, along with a validation report 3D structure visualizer for a huge number closer inspection of structures. Such as all the ''glycosyltransferases'' or ''nmr problematic structures''. Note that you can retrieve such lists by using [http://www.rcsb.org/pdb/search/advSearch.do advanced search in PDB]. Also bear in mind that each of these custom searches will be assigned a unique permanent web address, so you can access these results later on. Also a list of your last custom searches is provided for your convenient.
<br style="clearThe ''specifics page'' is accessible from the ''[[ValidatorDB:both" />Database_organization#Synopsis_page | synopsis page]]'', either via the '''Quick Lookup''' bar, or via any single entry in the tables from the '''Details by molecule''' and '''Details by PDB entry'''. Depending on how it was accessed, the '''specifics page''' might retrieve validation results for one or more molecules, a fact mentioned at the very top of the page.
=Specifics page=The validation results are accessible in tabular and graphical form via several tabs on the '''[[ValidatorDB]] specifics page''' is accessible from the [[ValidatorDB#Synopsis_page | synopsis page]], either via the namely '''LookUp barOverview''' on the , '''OverviewSummary''' tab, or via the residue names and PDB IDs in the interactive tables on the tabs '''Details by Residue''' and '''Details by PDB EntryProcessing Warnings''', respectively. Depending on how it was accessed, These are described in detail in their respective sections below. It is important to note that the '''specifics page''' might retrieve 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 or more residuesreport at a time, a fact mentioned at and allow easy navigation between these reports. The only exception is the very top of '''Overview''' tab, which presents the pagetotal statistics for all validated molecules, and not per annotation.
The '''[[ValidatorDB]]''' specifics page provides a straightforward report of the validation results, including a summary and detailed information in both tabular and graphical form, along with a 3D structure visualizer for closer inspection of the problematic structures. These reports are accessible via several tabs on the specifics page, namely '''Overview''', '''Summary''', '''Details''' and '''Processing Warnings'''. These are described in detail in the section below. Inspecting the tabular and graphical validation reports accessible on the specifics page is the most comfortable and effective way to evaluate the results. Additionally, you You may use the JSON Data download button at the top right corner of the specifics page in order to download the complete validation reports and perform any additional analyses on your own.
==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.
Note that this statistics can be downloaded in a *.csv format after clicking 'CSV' in the bottom right corner All color coding conventions are kept (<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>), and tool tips provide descriptions of the infographicseach graphical element.
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==Summary==
[[File:VDB_Residue_summary.PNG|thumb|right|500px|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.
On the '''{| class="wikitable" border="1" style="margin: 1em auto 1em auto;" |- |<!--Col1-->[[File:VDB_Residue_summary.PNG| 650px]] |<!--Col2-->[[ValidatorDBFile:VDB_Entry_summary.PNG| 650px]] |- |<!--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, the first view a recapitulation of the results is available in the 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''' tabof the ''specifics page'' for a '''single PDB entry''' allows easy navigation between annotation-based<br/> validation reports. For 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 validated residuevalidation analysis<br/> (completeness, chirality, advanced), the Summary tab provides an overview of potential issues encounteredand statistics for each problematic atom. |}
If more than one residue were validated in one runFirst, the model from wwPDB CCD is briefly described by name, molecular formula, 2D structure, etc. Next, a list recapitulation of these residues will be at the top all molecules and their respective PDB entries is also included, followed by a table with results of the pagemain validation analyses (completeness, chirality, advanced). In order to examine the For each validation summary analysis, statistics are provided for each residue, you will need to either click on all problematic atoms. Note that specific residue in here the list, or just scroll down statistics cover only the page till you reach it. Each validated residue is identified by its molecules sharing this annotation (3-letter code, as well as its chemical formula and common name. Validation statistics are given as absolute numbers and percentages over all the motifs that were processed for each residue).
The first table with the validation report results is organized into two main sections, referring to '''incomplete''' (''Missing Atoms'' or ''Rings'') and ''complete structures''. respectively. The section with ''complete structures''is further organized into subsections based on the results of the ' (''With All Atomschirality'' and ''Ringsadvanced'') respectivelyanalyses. The formal Specifically, a general distinction is made between ring atoms ''complete structures'' with ''correct chirality'' and non-ring atoms (simply denoted as atoms) is meant to allow a quick localization of potential issues in residues containing rings, especially where with ''wrong chirality''. Warnings like ''foreign atom identifiers are not useful. ''and 'Chirality'substitutions'' is evaluated only for the complete structures, since the absence of some atoms makes it difficult to check the chirality of some of the remaining atoms. Further, the problematic atoms are highlighted, in order to better localize the problems in the structuresalso included.
LastSubsequent tables highlight problematic atoms and provide useful statistics, a 2D representation of in order to better localize the problems in the model residuestructures. If you click on any validation issue (e.g., and missing rings, wrong chirality on a pie chart specific atom), you will be redirected to the '''Details''' tab where only the molecules with the validation results those specific issues are provided for visual representation purposeslisted. You Results can download them via be interpreted using the small icon at information in the top right corner [[ValidatorDB:Database_contents | Database contents]]. Tool tips are available for each element of the charttable headers. 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>, and later use them in your presentations<span style="color:#607d8b">warning</span>.
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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.]]
==Whereas the '''Summary''' tab of the ''synopsis page'' provides statistics, the '''Details==[[File:VDB_Residue_details''' tab allows you to filter the validation results according to the results of the various validation analyses.PNG|thumb|right|500px|Note that you may also access relevant information in the '''Details''' tab]]by clicking on a specific validation issue in any of the tables in the '''Summary''' tab.
Whereas The results acessible by the Summary '''Details''' tab provides statistics are organized into a table where each row contains information regarding a single ''validated molecule''. Which table columns are filled depends mostly on the state of the issues over all validated motifs for each validated residuefilter bar above the table (see description in the next paragraph). The most important columns are ''Id'', ''Issues'', ''Missing atoms/rings'', the ''Atoms'', 'Details'Processing warnings'' tab . The other columns give additional information, usually helpful in identifying the source of the error in the structure. The column ''Id''[[ValidatorDB]]refers to a unique identifier assigned to each individual ''validated molecule'' specifics page allows you in order to inspect keep a straightforward track of the molecule's origin. The ''Id'' contains the issues in select groups PDB ID, as well as the serial index of motifs, and further the first atom in each individual the corresponding ''input motif'' as it appears in the original PDB entry. Note that you may also access The column ''Issues'' reports the details number of any validation issues found for each particular group molecule. The column ''Missing atoms/rings'' explains which atoms are missing in each validated molecule, whereas ''Atoms'' shows the position of motifs also incorrect chirality. ''Missing atoms'' are listed by clicking their atom identifier in the ''model'', whereas atoms with wrong chirality are listed by their identifier in the ''validated molecule''. Clicking on a specific issue column header allows to sort the validated molecules according to the property specified in any the header. Validated molecules where a ''processing warning'Summary''' tab tablewas encountered are marked in <span style="color:#C68E17">color</span>. For further explanation, please refer to the sections on [[ValidatorDB:Terminology | terminology ]], [[ValidatorDB:Principles | principles ]] and [[ValidatorDB:Database_contents | database contents ]].
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.
Which table columns are filled depend mostly on Aside from its filtering function, the type of issue selected in the filter. The most important columns are ''Id'Details', ''Issues/Warnings'', ''Missing atoms/rings'', ''Atoms'', ''Processing warnings''also provides direct access to explicit validation reports for individual molecules. The other columns give additional information, usually helpful in identifying the source of the error in the structure. Note that complete structures '''do not''' contain columns with Just click on the information about missing atoms. The column Id refers to a (unique identifier assigned to each motif in order to keep a transparent trace of the motif's origin, as it contains containing the PDB ID, as well as the and a serial index of the first atom in the motif, as it appears in the original PDB entry. The column ''Issues/Warnings'' reports the number ) of issues or warnings found for each particular motif. The column ''Missing atoms/rings'' explains which atoms are missing in each validated motif, whereas ''Atoms'' shows the position molecule of incorrect chirality. ''Missing atoms'' are listed by their atom identifier interest in the model, whereas atoms with wrong chirality are listed by their identifier in the validated motif. Clicking on a column header allows order to sort the motifs according be redirected to the property specified in the headercorresponding validation report.
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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''' table of the ''specifics page''. Consists of a full description for the molecule and the model, complete with references, all results from all validation analyses, and 3Dvisualization of all structures involved in the validation process.]] The '''single molecule report''' offers a complete image of the validation results for each particular molecule. It is accessible via the ''' visualization Details''' tab on the ''specifics page'', by clicking on the Id (unique identifier containing the PDB ID and a serial number) of the molecule of interest. As you open this report, the molecule Id will appear in the top left corner of the report. The '''single molecule report''' starts with two 3D visualizers, where you can manipulate with the 3D representations of the validated molecule, the input motif, the model, and superimpositions of these, in order to better assess the position and detailed resultsrelevance of the structural issues found during validation (see the full list of terms [[ValidatorDB:Terminology | here]]). At 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, and is especially helpful for larger molecules.
The 3D viewer implemented in Beneath the [[ValidatorDB]] interface offers one step further in the analysis of each individual validated motifvisualizers, and is accessible via the '''Detailssingle molecule report''' tab on is organized into three columns, but you may have to scroll down to see all the specifics pageinformation in each column. In The left column contains the full identification of the tablemolecule in its original PDB entry, simply click on the Id description of the model and full identification in the wwPDB CCD, and a motif list of interest in order to open the 3D viewer[[ValidatorDB:Database_contents#Processing_warnings | processing warnings]], where you can inspect the structural inaccuracies more closelyif any were encountered during validation. Here you will be able to view and manipulate with The middle column lists the 3D representations results of the validated motif ''completeness'' and model residue''chirality'' analyses, to help you better assess and the position and relevance right column those of the structural issues found during ''advanced'' analyses (see the full list of validationanalyses [[ValidatorDB:Principles#Validation_analyses | here]]). Additionally, a 2D representation of the model Each problematic atom is provided for clarity, which is especially helpful for larger motifslisted. Basic information about The results are labeled using the validated motif is also givenunified color scheme: <span style="color:#006400">complete structure and correct chirality</span>, <span style="color:#FF0000">incomplete structure</span>, along with a complete report of the validation results<span style="color:#DAA520">wrong chirality</span>, where all the potential issues are listed<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.
Overally a Some '''Processing warnings''' are issues that may cause incorrect validation, such as two molecules being too close together in the 3D space, or some atoms being too far (disconnected) from the rest of the molecule. Such structures are generally marked as ''degenerate'' in the ''completeness'' analyses. Other '''processing warning may simply lead warnings''' are only meant to ignoring a faulty atominform of which course of action was taken during validation (e.g., but which conformer was validated if several conformers of that molecule were present in the original PDB entry). The drop down menu at the top of the page helps filter the motif is validatedwarnings for molecules with a specific annotation (3-letter code).
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'''Continue by examining the [[ValidatorDB:CaseStudies | case studies]], or return to the [[ValidatorDB:UserManual | Table of contents]].'''