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ValidatorDB:Database organization

2,741 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).
Whereas the '''Summary''' tab of the ''synopsis page'' provides statistics, the '''Details''' tab allows you to filter the validation results according to the results of the various validation analyses. 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.
The results acessible by the '''Details''' tab 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 filter bar above the table (see description in the next paragraph). The most important columns are ''Id'', ''Issues'', ''Missing atoms/rings'', ''Atoms'', ''Processing warnings''. The other columns give additional information, usually helpful in identifying the source of the error in the structure. The column ''Id'' refers to a unique identifier assigned to each individual ''validated molecule'' in order to keep a straightforward track of the molecule's origin. The ''Id'' contains the PDB ID, as well as the serial index of the first atom in the corresponding ''input motif'' as it appears in the original PDB entry. The column ''Issues'' reports the number of validation issues found for each particular molecule. The column ''Missing atoms/rings'' explains which atoms are missing in each validated molecule, whereas ''Atoms'' shows the position of incorrect chirality. ''Missing atoms'' are listed by their atom identifier in the ''model'', whereas atoms with wrong chirality are listed by their identifier in the ''validated molecule''. Clicking on a column header allows to sort the validated molecules according to the property specified in the header. Validated molecules where a ''processing warning'' was encountered are marked in orange<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 of the ''specifics page'' are organized by annotation (3-letter code). You can easily navigate between reports by selecting the annotation of interest in the leftmost drop down menu in the filter bar under the tab names (above the table). Only the table rows with results for the molecules that were matched to that annotation will be displayed. You may further refine the filter according to the 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 menu in the filter bar. Only the table rows with results for the molecules which exhibited that particular issue will be displayed. Whenever you pick something in a drop down menu of the filter bar, the number of molecules that fit your selection is given in brackets. If you want to make your selection even more specific, use the ''Id filter'' at the right of the filter bar.
Aside from its filtering function, the '''Details''' also provides direct access to explicit validation reports for individual molecules. Just click on the Id (unique identifier containing the PDB ID and a serial number) of the molecule of interest in order to be redirected to the corresponding validation report.
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==3D visualizationSingle molecule report==[[File:VDB_Details_entry.PNG|thumb|right|650px|'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|650px|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]].'''

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