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ValidatorDB:Database organization

6,024 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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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 '''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.  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.
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. You may use the JSON Data download button at the top right corner of the 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 the molecules you selected. 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. The green box above the graph indicates the number of validated molecules, together with their origin.
To keep consistency with the ''synopsis page'', the '''Overview''' tab on the ''specifics page'' also allows visualization of general validation statistics for the molecules you selected. 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 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 each graphical element.
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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]] |right<!--Col2-->[[File:VDB_Entry_summary.PNG| 650px]] |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. |}
On First, the '''[[ValidatorDB]]''' specifics pagemodel from wwPDB CCD is briefly described by name, the first view molecular formula, 2D structure, etc. Next, a recapitulation of the all molecules and their respective PDB entries is also included, followed by a table with results is available in of the '''Summary''' tabmain validation analyses (completeness, chirality, advanced). For each validated residuevalidation analysis, statistics are provided for all problematic atoms. Note that here the statistics cover only the Summary tab provides an overview of potential issues encounteredmolecules sharing this annotation (3-letter code).
If more than one residue were validated in one run, a list of these residues will be at the top of the page. In order to examine the The first table with validation summary for each residueresults is organized into two main sections, you will need referring to either click ''incomplete'' (''Missing Atoms'' or ''Rings'') and ''complete structures''. respectively. The section with ''complete structures'' is further organized into subsections based on that specific residue in the list, or just scroll down results of the page till you reach it''chirality'' and ''advanced'' analyses. Each validated residue Specifically, a general distinction is identified by its 3-letter code, as well as its chemical formula made between ''complete structures'' with ''correct chirality'' and common namewith ''wrong chirality''. Validation statistics Warnings like ''foreign atom'' and ''substitutions'' are given as absolute numbers and percentages over all the motifs that were processed for each residuealso included.
The table with the validation report is organized into two main sections, referring to '''incomplete''' (''Missing Atoms'' or ''Rings'') and '''complete structures''' (''With All Atoms'' and ''Rings'') respectively. The formal distinction between ring Subsequent tables highlight problematic atoms and non-ring atoms (simply denoted as atoms) is meant to allow a quick localization of potential issues in residues containing rings, especially where atom identifiers are not provide useful. '''Chirality''' 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 highlightedstatistics, in order to better localize the problems in the structures.
LastIf you click on any validation issue (e.g., missing rings, wrong chirality on a 2D representation of specific atom), you will be redirected to the '''Details''' tab where only the model residue, and a pie chart molecules with the validation results those specific issues are provided for visual representation purposeslisted. You  Results can download them via be interpreted using the information in the small icon at [[ValidatorDB:Database_contents | Database contents]]. Tool tips are available for each element of the top right corner table headers. The results for different types of validation analyses are labeled using the chartunified color scheme: <span style="color:#006400">complete structure and correct chirality</span>, and later use them in your presentations<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==
[[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''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.
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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