MotiveValidator:Service Organization

From WebChem Wiki
Jump to: navigation, search

Synopsis page

MotiveValidator-1.png MotiveValidator-2.png
The synopsis page consists of 5 tabs, one providing support, and three enabling access to the MotiveValidator service and one for downloading the binary for in-house use. The support tab Quick Help helps you get started, with basic information about how to get oriented in the web service. 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. First mode allows residue validation in the present release of the PDB. It might be worth trying to find out you the results in the ValidatorDB database.
MotiveValidator-3.png MotiveValidator-4.png
Sugar validation automatically identifies all carbohydrate residues in the input data and subsequently validates them Motif/Fragment Validation validates user-uploaded motifs. These can be extracted from PDB files using PatternQuery service.


Specifics page

The MotiveValidator specifics page provides detailed validation reports for various selections of the validation results. 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 after the calculation is completed. Depending on the validated molecules, 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.

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 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.

First, the brief details of the model (name, molecular formula, 2D structure, etc.) are given in case it comes from wwPDB CCD. 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 limitations, or return to the Table of contents.