ValidatorDB:Database organization

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

The synopsis page consists of 6 tabs, two providing support, and four enabling access to the database itself. Since this is your first contact with the database, the support tabs Quick Help and Samples help you get started, with basic information and examples of database snippets. Various interactive guides are accessible by a green button at the top right corner of some tabs. Examples of more complex analyses are available as case studies.

VDB intro.png
VDB samples.png
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. 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 case studies.

The ValidatorDB synopsis page further provides access to various data sets. You may retrieve specific validation reports using the Search tab. Further, the results from PDB-wide validations are available via three different tabs, namely Overview, Details by molecule and Details by PDB entry. A full description of each of these tab is given in their respective sections.


Search

The Search tab allows to retrieve validation reports for specific molecules. You may use several search criteria, namely by PDB entry (4-letter code), by molecule identifier (PDB ID: residue ID chain), molecule annotation (3-letter code), or a combination of the PDB entry and molecule annotation (shown here). In each case you will be provided with an input field, where you can enter a list of values for the relevant criterion. Examples and tool tips are provided for easy reference with respect to the expected syntax.

ValidatorDB contains validation results for the entire Protein Data Bank. You are probably interested only in a subset of these (e.g., the validation results for a specific inhibitor which appears in the PDB entry you plan to use further in your simulations). The synopsis page allows to access specific validation reports via the Search tab.

You may define the search using several criteria, namely PDB entry (4-letter code), molecule identifier (PDB ID: residue ID chain), molecule annotation (3-letter code), or a combination of the PDB entry and molecule annotation. The syntax of the search is quite simple, but you can always check out the examples and tool tips if you want to make sure.

Click on criterion you plan to use. In each case, there will be an input field where you can enter a comma or new line separated list of values for the relevant criterion. You may prefer to use the advanced search functions available on the Protein Data Bank web page, in order to generate a list of relevant annotations and PDB IDs. Instructions on how to achieve this are included in the web page as a tool tip.

Once you click the blue search button at the bottom of the page, the validation results for the molecules you specified according to the chosen criteria are then retrieved from ValidatorDB, organized and made accessible via a unique specifics page, which you can access at a later time via its unique URL. The specifics page is described in detail in the second part of the Data organization section of this manual.

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



Overview

The Overview tab contains an overall validation report for all the ligands and non-standard residues in the Protein Data Bank. Each bar represents overall statistics for the results of a certain type of validation analysis .

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

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

Results can be interpreted using the information in the Database contents. Tool tips are available for each element of the graph.

The results for different types of validation analyses are labeled using the unified color scheme: complete structure and correct chirality, incomplete structure, wrong chirality, warning.



Details by molecule

The Details by molecule tab contains an interactive table summarizing the results for sets of molecules sharing the same annotation (3-letter code). Each row recapitulates PDB-wide validation results for each such set of molecules. For a given annotation, each column gives the number or percentage of validated molecules which exhibited issues or fared well during a certain validation analysis .

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

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

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

Results can be interpreted using the information in the Database contents. Tool tips are available for each element of the table header.

The results for different types of validation analyses are labeled using the unified color scheme: complete structure and correct chirality, incomplete structure, wrong chirality, warning.

Details by PDB entry

The Details by PDB entry tab contains an interactive table summarizing the results for sets of molecules originating from the same PDB entry. Each row recapitulates the validation results for all relevant molecules in a single PDB entry. For a given PDB entry, each column gives the number or percentage of validated molecules which exhibited issues or fared well during a certain validation analysis .

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

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

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

Results can be interpreted using the information in the Database contents. Tool tips are available for each element of the table header.

The results for different types of validation analyses are labeled using the unified color scheme: complete structure and correct chirality, incomplete structure, wrong chirality, warning.


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 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.

You may use the JSON 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

The Overview tab of 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.

All color coding conventions are kept (complete structure and correct chirality, incomplete structure, wrong chirality, warning), and tool tips provide descriptions of each graphical element.


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.

VDB Residue summary.PNG VDB Entry summary.PNG
The Summary tab of the specifics page for all molecules sharing a specific annotation (3-letter code). The
report consists of a description of the model corresponding to that annotation, a recapitulation of all validated
molecules sharing that annotation, statistics for each validation analysis (completeness, chirality, advanced),
and statistics for each problematic atom.
The Summary tab of the specifics page for a single PDB entry allows easy navigation between annotation-based
validation reports. Each report consists of a description of the model corresponding to that annotation,
a recapitulation of all validated molecules sharing that annotation, statistics for each validation analysis
(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).

The first table with validation 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 chirality and advanced analyses. Specifically, a general distinction is made between complete structures with correct chirality and with wrong chirality. Warnings like foreign atom and substitutions are also included.

Subsequent tables highlight problematic atoms and provide useful statistics, in order to better localize the problems in the structures.

If you click on any validation issue (e.g., missing rings, wrong chirality on a specific atom), you will be redirected to the Details tab where only the molecules with those specific issues are listed.

Results can be interpreted using the information in the Database contents. Tool tips are available for each element of the table headers. The results for different types of validation analyses are labeled using the unified color scheme: complete structure and correct chirality, incomplete structure, wrong chirality, warning.

Details

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 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 color. For further explanation, please refer to the sections on terminology , principles and 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.


Single molecule report

'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 3D visualization 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 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 relevance of the structural issues found during validation (see the full list of terms 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.

Beneath the visualizers, the single molecule report is organized into three columns, but you may have to scroll down to see all the information in each column. The left column contains the full identification of the molecule in its original PDB entry, the description of the model and full identification in the wwPDB CCD, and a list of processing warnings, if any were encountered during validation. The middle column lists the results of the completeness and chirality analyses, and the right column those of the advanced analyses (see the full list of validation analyses here). Each problematic atom is listed. The results are labeled using the unified color scheme: complete structure and correct chirality, incomplete structure, wrong chirality, warning.


Processing Warnings

The Processing warnings tab of the specifics page lists unusual circumstances encountered during validation.

The specifics page may also contain the separate tab Processing warnings, which lists unusual circumstances encountered during the validation of each molecule. Sometimes the PDB entries contain information that is ambiguous, conflicting or which deviates strongly from the expected reference.

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 warnings are only meant to inform of which course of action was taken during validation (e.g., 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 warnings for molecules with a specific annotation (3-letter code).

Continue by examining the case studies, or return to the Table of contents.