Results Analysis - Global Properties

Once you got a quick overview of some key descriptors in the Overview page, you can open the Global Properties tab in your results page.

Opening the tab will display the full list of all antibodies in your prediction

Each antibody of your input is reported in a dedicated line in the report. You'll have a reminder of the identifiers, the class of antibody modelled, the Patch Map and the CDR sequences of both heavy & light chains.

In the appendix below you can find a full list and description of all properties available in the default report.

Download

In the first column of the report you have download icons to download either the full set or individual predictions. You can choose between these download formats:

• PDB file (structure of the initial model built from sequence or your initial structure)
• MOE database (mdb file containing the final output from the property calculations
• MOE ensemble database (mdb file containing all snapshots and details of the ensemble based property calculations)
• Fasta file (your input sequences as they were analyzed by the platform)
• Excel file (of the table you see on the screen)
• CSV file (of the data you see on the screen)

Actions on column headers

In every table in 3dpredict you can trigger actions directly from the column headers, like sorting & filtering or reordering columns.

When hovering a particular column with your mouse allows you to display an up & down arrow. Clicking them will trigger an alphanumerical sort of the column.
You might also spot the dotted area in front of the Column name. That's a dragging area that allows you to quickly grab the column (click & hold your left mouse button) and drag it to another location in the table. This allows you to order columns the way you want.
When doing a single click on the title text of the column you'll see a little popup appear. This popup allows you to freeze your column (in the order of columns and all before that), or drop the column from the view (hide it via the icon with the column & the little x next to it). Below you also have the possibility to add text to quickly filter your table for any text that matches text found in that column

If you run a text filter and hit enter you'll see a section showing above the table. This section lists all filtering & coloring options you currently have applied to your table. You can enable or disable them by clicking on the checkbox in front of them. If you want to delete the filter, click on the x icon on the right.

Table actions

At the top of each table in the application you should see all or parts of these items:

1. a text search allowing to filter your table by any text you type (molecule identifier, sequence portion of the CDR sequences, Germlines, Liabilities (on the liability page). Activating this will creae a filter like we've covered in the previous paragraph.
2. Report Selection Box: Here it shows (and by default it does) "Primary Report". A report in 3dpredict/Ab is a particular view on your data that either has been set up for you or that you customized. So any setting, filtering, coloring, column sorting & hiding can be saved as a report for your later use. This allows you to set up the view the way you want it. If you click on the primary report combo box, you will see all reports that are available and that have been created either by you or by power users of your tenant. you can change the report that you would like to display by selecting another report, and you will see your default view change. Let's, for instance, select the Global report with confidence intervals: You can see now that columns with numerical values have the Boltzmann-averaged value, like in the previous report, but also 95% confidence intervals, which are part of this reports column selections.
3. In the report combo box, you have an actions menu that allows you to access several actions you can do within the report

Actions menu

Columns

Adjust which columns to show or hide & their order

The dialog allows you to select which columns to display, and the arrow buttons in the bottom allow you to shift up and down according to the ordering of the columns that you would like to have. The right-hand side of the panel allows you to adjust the name of the column and the column width that you would like to have for this column.

Filter

To filter data by numerical values, you can select the filter option in the actions menu and define your column that you want to filter by. Here it's: patch cdr hyd.

You can then choose an operator (less than, greater than, equals, between)

and the value you want to filter by.

This dialog also allows you to filter by text a full row. Here a text search is undertaken and filtered by the found text anywhere in any column of that particular row. Here we search for GTT which is part of one of the CDR regions of one of the sequences in our set.

The resulting table shows only the row of the dataset that contains the GTT motif in CDR H2.

Format

The highlight dialog allows you to highlight and color particular rows or columns according to some conditions that you can specify

On the left-hand side of the dialog, you have the list of all the highlights that you want to specify and order. If you want to add another one, you click on the plus icon. If you want to drop one, you click on the minus icon. On the right-hand side, you have the details of one particular highlight. Here, CDR ID gives a name. You specify what type of object to highlight: the row or the column and which column to highlight (here Patch CDR Hyd). Next, you can specify which background and text color to apply for the highlight and what condition should be met in order to highlight or apply the highlighting to the column. Here, we chose that the column patch CDR-Hyd should contain a value that is less than 400.

Once you click save we can see that the report now contains a highlighted section at the top that you can edit again, enable, and disable. Our patch CDR Hyd values below 400 are colored in green.

The highlight can also be applied to the full row in the data table.
In order to do so you need to select "Highlight" Row in the dialog.

If you want now to color rows in a certain colour and columns according to another one you can also achieve that in the set up dialog.

You can add different coloring rules on top of each other and resulting in overlapping colorings. The order of the coloring rules will have an impact on what is rendered above what in the final report.

Here we show the column based coloring in front of the row based one.

Selection

The actions menu also has an item called selection allowing you to interact with selected rows in your table. You can select rows by simply clicking on a row, clicking on the checkboxes in the first column, or by clicking in a row and using shift + click to select multiple rows between the two clicks. Ctrl (Cmd on mac) + clicks allows to specifically select the clicked rows.
Once they are selected you can copy the selected row into the your clipboard using the Actions -> copy to clipboard button.
You can also choose your selected rows to be added or the basis of a new collection. Briefly, collections allow you to persist particular molecules across different jobs and conveniently drag them into your new reports to compare between your new molecules and reference molecules you added to collections.

Report

A report in the application represents all the visual preferences you have applied on your table so far. You can prepare these preferences in a one-shot session, but the next time you connect they'll be reset to the applications default. If you want to visualize your data systematically the same way you can use the report -> save as menu allowing you to save your current view.

As user can only save your report privately for your own use. Give it a name, here " No Parental" and click save.

Now in the report selection box above the table you have your new report selected. At any time when coming back later you'll have access to that report.
NB: reports do not save data but visual preferences & filters. So you can apply reports to new & old jobs across your data.
If you are a power user of 3dpredict/Ab you have the right to save reports as public reports. These are then shared with all users of your organization.

Appendix

Properties